Client-Side Event Processing for Personalized Web Advertisement

NASA Astrophysics Data System (ADS)

Stühmer, Roland; Anicic, Darko; Sen, Sinan; Ma, Jun; Schmidt, Kay-Uwe; Stojanovic, Nenad

The market for Web advertisement is continuously growing and correspondingly, the number of approaches that can be used for realizing Web advertisement are increasing. However, current approaches fail to generate very personalized ads for a current Web user that is visiting a particular Web content. They mainly try to develop a profile based on the content of that Web page or on a long-term user's profile, by not taking into account current user's preferences. We argue that by discovering a user's interest from his current Web behavior we can support the process of ad generation, especially the relevance of an ad for the user. In this paper we present the conceptual architecture and implementation of such an approach. The approach is based on the extraction of simple events from the user interaction with a Web page and their combination in order to discover the user's interests. We use semantic technologies in order to build such an interpretation out of many simple events. We present results from preliminary evaluation studies. The main contribution of the paper is a very efficient, semantic-based client-side architecture for generating and combining Web events. The architecture ensures the agility of the whole advertisement system, by complexly processing events on the client. In general, this work contributes to the realization of new, event-driven applications for the (Semantic) Web.

Graph-Based Semantic Web Service Composition for Healthcare Data Integration.

PubMed

Arch-Int, Ngamnij; Arch-Int, Somjit; Sonsilphong, Suphachoke; Wanchai, Paweena

2017-01-01

Within the numerous and heterogeneous web services offered through different sources, automatic web services composition is the most convenient method for building complex business processes that permit invocation of multiple existing atomic services. The current solutions in functional web services composition lack autonomous queries of semantic matches within the parameters of web services, which are necessary in the composition of large-scale related services. In this paper, we propose a graph-based Semantic Web Services composition system consisting of two subsystems: management time and run time. The management-time subsystem is responsible for dependency graph preparation in which a dependency graph of related services is generated automatically according to the proposed semantic matchmaking rules. The run-time subsystem is responsible for discovering the potential web services and nonredundant web services composition of a user's query using a graph-based searching algorithm. The proposed approach was applied to healthcare data integration in different health organizations and was evaluated according to two aspects: execution time measurement and correctness measurement.

Graph-Based Semantic Web Service Composition for Healthcare Data Integration

PubMed Central

2017-01-01

Within the numerous and heterogeneous web services offered through different sources, automatic web services composition is the most convenient method for building complex business processes that permit invocation of multiple existing atomic services. The current solutions in functional web services composition lack autonomous queries of semantic matches within the parameters of web services, which are necessary in the composition of large-scale related services. In this paper, we propose a graph-based Semantic Web Services composition system consisting of two subsystems: management time and run time. The management-time subsystem is responsible for dependency graph preparation in which a dependency graph of related services is generated automatically according to the proposed semantic matchmaking rules. The run-time subsystem is responsible for discovering the potential web services and nonredundant web services composition of a user's query using a graph-based searching algorithm. The proposed approach was applied to healthcare data integration in different health organizations and was evaluated according to two aspects: execution time measurement and correctness measurement. PMID:29065602

Semantic Web Services Challenge, Results from the First Year. Series: Semantic Web And Beyond, Volume 8.

NASA Astrophysics Data System (ADS)

Petrie, C.; Margaria, T.; Lausen, H.; Zaremba, M.

Explores trade-offs among existing approaches. Reveals strengths and weaknesses of proposed approaches, as well as which aspects of the problem are not yet covered. Introduces software engineering approach to evaluating semantic web services. Service-Oriented Computing is one of the most promising software engineering trends because of the potential to reduce the programming effort for future distributed industrial systems. However, only a small part of this potential rests on the standardization of tools offered by the web services stack. The larger part of this potential rests upon the development of sufficient semantics to automate service orchestration. Currently there are many different approaches to semantic web service descriptions and many frameworks built around them. A common understanding, evaluation scheme, and test bed to compare and classify these frameworks in terms of their capabilities and shortcomings, is necessary to make progress in developing the full potential of Service-Oriented Computing. The Semantic Web Services Challenge is an open source initiative that provides a public evaluation and certification of multiple frameworks on common industrially-relevant problem sets. This edited volume reports on the first results in developing common understanding of the various technologies intended to facilitate the automation of mediation, choreography and discovery for Web Services using semantic annotations. Semantic Web Services Challenge: Results from the First Year is designed for a professional audience composed of practitioners and researchers in industry. Professionals can use this book to evaluate SWS technology for their potential practical use. The book is also suitable for advanced-level students in computer science.

Semantic web data warehousing for caGrid.

PubMed

McCusker, James P; Phillips, Joshua A; González Beltrán, Alejandra; Finkelstein, Anthony; Krauthammer, Michael

2009-10-01

The National Cancer Institute (NCI) is developing caGrid as a means for sharing cancer-related data and services. As more data sets become available on caGrid, we need effective ways of accessing and integrating this information. Although the data models exposed on caGrid are semantically well annotated, it is currently up to the caGrid client to infer relationships between the different models and their classes. In this paper, we present a Semantic Web-based data warehouse (Corvus) for creating relationships among caGrid models. This is accomplished through the transformation of semantically-annotated caBIG Unified Modeling Language (UML) information models into Web Ontology Language (OWL) ontologies that preserve those semantics. We demonstrate the validity of the approach by Semantic Extraction, Transformation and Loading (SETL) of data from two caGrid data sources, caTissue and caArray, as well as alignment and query of those sources in Corvus. We argue that semantic integration is necessary for integration of data from distributed web services and that Corvus is a useful way of accomplishing this. Our approach is generalizable and of broad utility to researchers facing similar integration challenges.

Advancing translational research with the Semantic Web.

PubMed

Ruttenberg, Alan; Clark, Tim; Bug, William; Samwald, Matthias; Bodenreider, Olivier; Chen, Helen; Doherty, Donald; Forsberg, Kerstin; Gao, Yong; Kashyap, Vipul; Kinoshita, June; Luciano, Joanne; Marshall, M Scott; Ogbuji, Chimezie; Rees, Jonathan; Stephens, Susie; Wong, Gwendolyn T; Wu, Elizabeth; Zaccagnini, Davide; Hongsermeier, Tonya; Neumann, Eric; Herman, Ivan; Cheung, Kei-Hoi

2007-05-09

A fundamental goal of the U.S. National Institute of Health (NIH) "Roadmap" is to strengthen Translational Research, defined as the movement of discoveries in basic research to application at the clinical level. A significant barrier to translational research is the lack of uniformly structured data across related biomedical domains. The Semantic Web is an extension of the current Web that enables navigation and meaningful use of digital resources by automatic processes. It is based on common formats that support aggregation and integration of data drawn from diverse sources. A variety of technologies have been built on this foundation that, together, support identifying, representing, and reasoning across a wide range of biomedical data. The Semantic Web Health Care and Life Sciences Interest Group (HCLSIG), set up within the framework of the World Wide Web Consortium, was launched to explore the application of these technologies in a variety of areas. Subgroups focus on making biomedical data available in RDF, working with biomedical ontologies, prototyping clinical decision support systems, working on drug safety and efficacy communication, and supporting disease researchers navigating and annotating the large amount of potentially relevant literature. We present a scenario that shows the value of the information environment the Semantic Web can support for aiding neuroscience researchers. We then report on several projects by members of the HCLSIG, in the process illustrating the range of Semantic Web technologies that have applications in areas of biomedicine. Semantic Web technologies present both promise and challenges. Current tools and standards are already adequate to implement components of the bench-to-bedside vision. On the other hand, these technologies are young. Gaps in standards and implementations still exist and adoption is limited by typical problems with early technology, such as the need for a critical mass of practitioners and installed base, and growing pains as the technology is scaled up. Still, the potential of interoperable knowledge sources for biomedicine, at the scale of the World Wide Web, merits continued work.

Advancing translational research with the Semantic Web

PubMed Central

Ruttenberg, Alan; Clark, Tim; Bug, William; Samwald, Matthias; Bodenreider, Olivier; Chen, Helen; Doherty, Donald; Forsberg, Kerstin; Gao, Yong; Kashyap, Vipul; Kinoshita, June; Luciano, Joanne; Marshall, M Scott; Ogbuji, Chimezie; Rees, Jonathan; Stephens, Susie; Wong, Gwendolyn T; Wu, Elizabeth; Zaccagnini, Davide; Hongsermeier, Tonya; Neumann, Eric; Herman, Ivan; Cheung, Kei-Hoi

2007-01-01

Background A fundamental goal of the U.S. National Institute of Health (NIH) "Roadmap" is to strengthen Translational Research, defined as the movement of discoveries in basic research to application at the clinical level. A significant barrier to translational research is the lack of uniformly structured data across related biomedical domains. The Semantic Web is an extension of the current Web that enables navigation and meaningful use of digital resources by automatic processes. It is based on common formats that support aggregation and integration of data drawn from diverse sources. A variety of technologies have been built on this foundation that, together, support identifying, representing, and reasoning across a wide range of biomedical data. The Semantic Web Health Care and Life Sciences Interest Group (HCLSIG), set up within the framework of the World Wide Web Consortium, was launched to explore the application of these technologies in a variety of areas. Subgroups focus on making biomedical data available in RDF, working with biomedical ontologies, prototyping clinical decision support systems, working on drug safety and efficacy communication, and supporting disease researchers navigating and annotating the large amount of potentially relevant literature. Results We present a scenario that shows the value of the information environment the Semantic Web can support for aiding neuroscience researchers. We then report on several projects by members of the HCLSIG, in the process illustrating the range of Semantic Web technologies that have applications in areas of biomedicine. Conclusion Semantic Web technologies present both promise and challenges. Current tools and standards are already adequate to implement components of the bench-to-bedside vision. On the other hand, these technologies are young. Gaps in standards and implementations still exist and adoption is limited by typical problems with early technology, such as the need for a critical mass of practitioners and installed base, and growing pains as the technology is scaled up. Still, the potential of interoperable knowledge sources for biomedicine, at the scale of the World Wide Web, merits continued work. PMID:17493285

GoWeb: a semantic search engine for the life science web.

PubMed

Dietze, Heiko; Schroeder, Michael

2009-10-01

Current search engines are keyword-based. Semantic technologies promise a next generation of semantic search engines, which will be able to answer questions. Current approaches either apply natural language processing to unstructured text or they assume the existence of structured statements over which they can reason. Here, we introduce a third approach, GoWeb, which combines classical keyword-based Web search with text-mining and ontologies to navigate large results sets and facilitate question answering. We evaluate GoWeb on three benchmarks of questions on genes and functions, on symptoms and diseases, and on proteins and diseases. The first benchmark is based on the BioCreAtivE 1 Task 2 and links 457 gene names with 1352 functions. GoWeb finds 58% of the functional GeneOntology annotations. The second benchmark is based on 26 case reports and links symptoms with diseases. GoWeb achieves 77% success rate improving an existing approach by nearly 20%. The third benchmark is based on 28 questions in the TREC genomics challenge and links proteins to diseases. GoWeb achieves a success rate of 79%. GoWeb's combination of classical Web search with text-mining and ontologies is a first step towards answering questions in the biomedical domain. GoWeb is online at: http://www.gopubmed.org/goweb.

Semantic web data warehousing for caGrid

PubMed Central

McCusker, James P; Phillips, Joshua A; Beltrán, Alejandra González; Finkelstein, Anthony; Krauthammer, Michael

2009-01-01

The National Cancer Institute (NCI) is developing caGrid as a means for sharing cancer-related data and services. As more data sets become available on caGrid, we need effective ways of accessing and integrating this information. Although the data models exposed on caGrid are semantically well annotated, it is currently up to the caGrid client to infer relationships between the different models and their classes. In this paper, we present a Semantic Web-based data warehouse (Corvus) for creating relationships among caGrid models. This is accomplished through the transformation of semantically-annotated caBIG® Unified Modeling Language (UML) information models into Web Ontology Language (OWL) ontologies that preserve those semantics. We demonstrate the validity of the approach by Semantic Extraction, Transformation and Loading (SETL) of data from two caGrid data sources, caTissue and caArray, as well as alignment and query of those sources in Corvus. We argue that semantic integration is necessary for integration of data from distributed web services and that Corvus is a useful way of accomplishing this. Our approach is generalizable and of broad utility to researchers facing similar integration challenges. PMID:19796399

Ubiquitous Computing Services Discovery and Execution Using a Novel Intelligent Web Services Algorithm

PubMed Central

Choi, Okkyung; Han, SangYong

2007-01-01

Ubiquitous Computing makes it possible to determine in real time the location and situations of service requesters in a web service environment as it enables access to computers at any time and in any place. Though research on various aspects of ubiquitous commerce is progressing at enterprises and research centers, both domestically and overseas, analysis of a customer's personal preferences based on semantic web and rule based services using semantics is not currently being conducted. This paper proposes a Ubiquitous Computing Services System that enables a rule based search as well as semantics based search to support the fact that the electronic space and the physical space can be combined into one and the real time search for web services and the construction of efficient web services thus become possible.

The semantic web in translational medicine: current applications and future directions

PubMed Central

Machado, Catia M.; Rebholz-Schuhmann, Dietrich; Freitas, Ana T.; Couto, Francisco M.

2015-01-01

Semantic web technologies offer an approach to data integration and sharing, even for resources developed independently or broadly distributed across the web. This approach is particularly suitable for scientific domains that profit from large amounts of data that reside in the public domain and that have to be exploited in combination. Translational medicine is such a domain, which in addition has to integrate private data from the clinical domain with proprietary data from the pharmaceutical domain. In this survey, we present the results of our analysis of translational medicine solutions that follow a semantic web approach. We assessed these solutions in terms of their target medical use case; the resources covered to achieve their objectives; and their use of existing semantic web resources for the purposes of data sharing, data interoperability and knowledge discovery. The semantic web technologies seem to fulfill their role in facilitating the integration and exploration of data from disparate sources, but it is also clear that simply using them is not enough. It is fundamental to reuse resources, to define mappings between resources, to share data and knowledge. All these aspects allow the instantiation of translational medicine at the semantic web-scale, thus resulting in a network of solutions that can share resources for a faster transfer of new scientific results into the clinical practice. The envisioned network of translational medicine solutions is on its way, but it still requires resolving the challenges of sharing protected data and of integrating semantic-driven technologies into the clinical practice. PMID:24197933

The semantic web in translational medicine: current applications and future directions.

PubMed

Machado, Catia M; Rebholz-Schuhmann, Dietrich; Freitas, Ana T; Couto, Francisco M

2015-01-01

Semantic web technologies offer an approach to data integration and sharing, even for resources developed independently or broadly distributed across the web. This approach is particularly suitable for scientific domains that profit from large amounts of data that reside in the public domain and that have to be exploited in combination. Translational medicine is such a domain, which in addition has to integrate private data from the clinical domain with proprietary data from the pharmaceutical domain. In this survey, we present the results of our analysis of translational medicine solutions that follow a semantic web approach. We assessed these solutions in terms of their target medical use case; the resources covered to achieve their objectives; and their use of existing semantic web resources for the purposes of data sharing, data interoperability and knowledge discovery. The semantic web technologies seem to fulfill their role in facilitating the integration and exploration of data from disparate sources, but it is also clear that simply using them is not enough. It is fundamental to reuse resources, to define mappings between resources, to share data and knowledge. All these aspects allow the instantiation of translational medicine at the semantic web-scale, thus resulting in a network of solutions that can share resources for a faster transfer of new scientific results into the clinical practice. The envisioned network of translational medicine solutions is on its way, but it still requires resolving the challenges of sharing protected data and of integrating semantic-driven technologies into the clinical practice. © The Author 2013. Published by Oxford University Press.

A Method for Transforming Existing Web Service Descriptions into an Enhanced Semantic Web Service Framework

NASA Astrophysics Data System (ADS)

Du, Xiaofeng; Song, William; Munro, Malcolm

Web Services as a new distributed system technology has been widely adopted by industries in the areas, such as enterprise application integration (EAI), business process management (BPM), and virtual organisation (VO). However, lack of semantics in the current Web Service standards has been a major barrier in service discovery and composition. In this chapter, we propose an enhanced context-based semantic service description framework (CbSSDF+) that tackles the problem and improves the flexibility of service discovery and the correctness of generated composite services. We also provide an agile transformation method to demonstrate how the various formats of Web Service descriptions on the Web can be managed and renovated step by step into CbSSDF+ based service description without large amount of engineering work. At the end of the chapter, we evaluate the applicability of the transformation method and the effectiveness of CbSSDF+ through a series of experiments.

Learning the Language of Healthcare Enabling Semantic Web Technology in CHCS

DTIC Science & Technology

2013-09-01

tuples”, (subject, predicate, object), to relate data and achieve semantic interoperability . Other similar technologies exist, but their... Semantic Healthcare repository [5]. Ultimately, both of our data approaches were successful. However, our current test system is based on the CPRS demo...to extract system dependencies and workflows; to extract semantically related patient data ; and to browse patient- centric views into the system . We

A Semantic Grid Oriented to E-Tourism

NASA Astrophysics Data System (ADS)

Zhang, Xiao Ming

With increasing complexity of tourism business models and tasks, there is a clear need of the next generation e-Tourism infrastructure to support flexible automation, integration, computation, storage, and collaboration. Currently several enabling technologies such as semantic Web, Web service, agent and grid computing have been applied in the different e-Tourism applications, however there is no a unified framework to be able to integrate all of them. So this paper presents a promising e-Tourism framework based on emerging semantic grid, in which a number of key design issues are discussed including architecture, ontologies structure, semantic reconciliation, service and resource discovery, role based authorization and intelligent agent. The paper finally provides the implementation of the framework.

Semantic computing and language knowledge bases

NASA Astrophysics Data System (ADS)

Wang, Lei; Wang, Houfeng; Yu, Shiwen

2017-09-01

As the proposition of the next-generation Web - semantic Web, semantic computing has been drawing more and more attention within the circle and the industries. A lot of research has been conducted on the theory and methodology of the subject, and potential applications have also been investigated and proposed in many fields. The progress of semantic computing made so far cannot be detached from its supporting pivot - language resources, for instance, language knowledge bases. This paper proposes three perspectives of semantic computing from a macro view and describes the current status of affairs about the construction of language knowledge bases and the related research and applications that have been carried out on the basis of these resources via a case study in the Institute of Computational Linguistics at Peking University.

Applying Semantic Web Services and Wireless Sensor Networks for System Integration

NASA Astrophysics Data System (ADS)

Berkenbrock, Gian Ricardo; Hirata, Celso Massaki; de Oliveira Júnior, Frederico Guilherme Álvares; de Oliveira, José Maria Parente

In environments like factories, buildings, and homes automation services tend to often change during their lifetime. Changes are concerned to business rules, process optimization, cost reduction, and so on. It is important to provide a smooth and straightforward way to deal with these changes so that could be handled in a faster and low cost manner. Some prominent solutions use the flexibility of Wireless Sensor Networks and the meaningful description of Semantic Web Services to provide service integration. In this work, we give an overview of current solutions for machinery integration that combine both technologies as well as a discussion about some perspectives and open issues when applying Wireless Sensor Networks and Semantic Web Services for automation services integration.

SSWAP: A Simple Semantic Web Architecture and Protocol for Semantic Web Services

USDA-ARS?s Scientific Manuscript database

SSWAP (Simple Semantic Web Architecture and Protocol) is an architecture, protocol, and platform for using reasoning to semantically integrate heterogeneous disparate data and services on the web. SSWAP is the driving technology behind the Virtual Plant Information Network, an NSF-funded semantic w...

Sharing Human-Generated Observations by Integrating HMI and the Semantic Sensor Web

PubMed Central

Sigüenza, Álvaro; Díaz-Pardo, David; Bernat, Jesús; Vancea, Vasile; Blanco, José Luis; Conejero, David; Gómez, Luis Hernández

2012-01-01

Current “Internet of Things” concepts point to a future where connected objects gather meaningful information about their environment and share it with other objects and people. In particular, objects embedding Human Machine Interaction (HMI), such as mobile devices and, increasingly, connected vehicles, home appliances, urban interactive infrastructures, etc., may not only be conceived as sources of sensor information, but, through interaction with their users, they can also produce highly valuable context-aware human-generated observations. We believe that the great promise offered by combining and sharing all of the different sources of information available can be realized through the integration of HMI and Semantic Sensor Web technologies. This paper presents a technological framework that harmonizes two of the most influential HMI and Sensor Web initiatives: the W3C's Multimodal Architecture and Interfaces (MMI) and the Open Geospatial Consortium (OGC) Sensor Web Enablement (SWE) with its semantic extension, respectively. Although the proposed framework is general enough to be applied in a variety of connected objects integrating HMI, a particular development is presented for a connected car scenario where drivers' observations about the traffic or their environment are shared across the Semantic Sensor Web. For implementation and evaluation purposes an on-board OSGi (Open Services Gateway Initiative) architecture was built, integrating several available HMI, Sensor Web and Semantic Web technologies. A technical performance test and a conceptual validation of the scenario with potential users are reported, with results suggesting the approach is sound. PMID:22778643

Sharing human-generated observations by integrating HMI and the Semantic Sensor Web.

PubMed

Sigüenza, Alvaro; Díaz-Pardo, David; Bernat, Jesús; Vancea, Vasile; Blanco, José Luis; Conejero, David; Gómez, Luis Hernández

2012-01-01

Current "Internet of Things" concepts point to a future where connected objects gather meaningful information about their environment and share it with other objects and people. In particular, objects embedding Human Machine Interaction (HMI), such as mobile devices and, increasingly, connected vehicles, home appliances, urban interactive infrastructures, etc., may not only be conceived as sources of sensor information, but, through interaction with their users, they can also produce highly valuable context-aware human-generated observations. We believe that the great promise offered by combining and sharing all of the different sources of information available can be realized through the integration of HMI and Semantic Sensor Web technologies. This paper presents a technological framework that harmonizes two of the most influential HMI and Sensor Web initiatives: the W3C's Multimodal Architecture and Interfaces (MMI) and the Open Geospatial Consortium (OGC) Sensor Web Enablement (SWE) with its semantic extension, respectively. Although the proposed framework is general enough to be applied in a variety of connected objects integrating HMI, a particular development is presented for a connected car scenario where drivers' observations about the traffic or their environment are shared across the Semantic Sensor Web. For implementation and evaluation purposes an on-board OSGi (Open Services Gateway Initiative) architecture was built, integrating several available HMI, Sensor Web and Semantic Web technologies. A technical performance test and a conceptual validation of the scenario with potential users are reported, with results suggesting the approach is sound.

Knowledge-Base Semantic Gap Analysis for the Vulnerability Detection

NASA Astrophysics Data System (ADS)

Wu, Raymond; Seki, Keisuke; Sakamoto, Ryusuke; Hisada, Masayuki

Web security became an alert in internet computing. To cope with ever-rising security complexity, semantic analysis is proposed to fill-in the gap that the current approaches fail to commit. Conventional methods limit their focus to the physical source codes instead of the abstraction of semantics. It bypasses new types of vulnerability and causes tremendous business loss.

Building the Knowledge Base to Support the Automatic Animation Generation of Chinese Traditional Architecture

NASA Astrophysics Data System (ADS)

Wei, Gongjin; Bai, Weijing; Yin, Meifang; Zhang, Songmao

We present a practice of applying the Semantic Web technologies in the domain of Chinese traditional architecture. A knowledge base consisting of one ontology and four rule bases is built to support the automatic generation of animations that demonstrate the construction of various Chinese timber structures based on the user's input. Different Semantic Web formalisms are used, e.g., OWL DL, SWRL and Jess, to capture the domain knowledge, including the wooden components needed for a given building, construction sequence, and the 3D size and position of every piece of wood. Our experience in exploiting the current Semantic Web technologies in real-world application systems indicates their prominent advantages (such as the reasoning facilities and modeling tools) as well as the limitations (such as low efficiency).

Linked Registries: Connecting Rare Diseases Patient Registries through a Semantic Web Layer

PubMed Central

González-Castro, Lorena; Carta, Claudio; van der Horst, Eelke; Lopes, Pedro; Kaliyaperumal, Rajaram; Thompson, Mark; Thompson, Rachel; Queralt-Rosinach, Núria; Lopez, Estrella; Wood, Libby; Robertson, Agata; Lamanna, Claudia; Gilling, Mette; Orth, Michael; Merino-Martinez, Roxana; Taruscio, Domenica; Lochmüller, Hanns

2017-01-01

Patient registries are an essential tool to increase current knowledge regarding rare diseases. Understanding these data is a vital step to improve patient treatments and to create the most adequate tools for personalized medicine. However, the growing number of disease-specific patient registries brings also new technical challenges. Usually, these systems are developed as closed data silos, with independent formats and models, lacking comprehensive mechanisms to enable data sharing. To tackle these challenges, we developed a Semantic Web based solution that allows connecting distributed and heterogeneous registries, enabling the federation of knowledge between multiple independent environments. This semantic layer creates a holistic view over a set of anonymised registries, supporting semantic data representation, integrated access, and querying. The implemented system gave us the opportunity to answer challenging questions across disperse rare disease patient registries. The interconnection between those registries using Semantic Web technologies benefits our final solution in a way that we can query single or multiple instances according to our needs. The outcome is a unique semantic layer, connecting miscellaneous registries and delivering a lightweight holistic perspective over the wealth of knowledge stemming from linked rare disease patient registries. PMID:29214177

Linked Registries: Connecting Rare Diseases Patient Registries through a Semantic Web Layer.

PubMed

Sernadela, Pedro; González-Castro, Lorena; Carta, Claudio; van der Horst, Eelke; Lopes, Pedro; Kaliyaperumal, Rajaram; Thompson, Mark; Thompson, Rachel; Queralt-Rosinach, Núria; Lopez, Estrella; Wood, Libby; Robertson, Agata; Lamanna, Claudia; Gilling, Mette; Orth, Michael; Merino-Martinez, Roxana; Posada, Manuel; Taruscio, Domenica; Lochmüller, Hanns; Robinson, Peter; Roos, Marco; Oliveira, José Luís

2017-01-01

Patient registries are an essential tool to increase current knowledge regarding rare diseases. Understanding these data is a vital step to improve patient treatments and to create the most adequate tools for personalized medicine. However, the growing number of disease-specific patient registries brings also new technical challenges. Usually, these systems are developed as closed data silos, with independent formats and models, lacking comprehensive mechanisms to enable data sharing. To tackle these challenges, we developed a Semantic Web based solution that allows connecting distributed and heterogeneous registries, enabling the federation of knowledge between multiple independent environments. This semantic layer creates a holistic view over a set of anonymised registries, supporting semantic data representation, integrated access, and querying. The implemented system gave us the opportunity to answer challenging questions across disperse rare disease patient registries. The interconnection between those registries using Semantic Web technologies benefits our final solution in a way that we can query single or multiple instances according to our needs. The outcome is a unique semantic layer, connecting miscellaneous registries and delivering a lightweight holistic perspective over the wealth of knowledge stemming from linked rare disease patient registries.

DOORS to the semantic web and grid with a PORTAL for biomedical computing.

PubMed

Taswell, Carl

2008-03-01

The semantic web remains in the early stages of development. It has not yet achieved the goals envisioned by its founders as a pervasive web of distributed knowledge and intelligence. Success will be attained when a dynamic synergism can be created between people and a sufficient number of infrastructure systems and tools for the semantic web in analogy with those for the original web. The domain name system (DNS), web browsers, and the benefits of publishing web pages motivated many people to register domain names and publish web sites on the original web. An analogous resource label system, semantic search applications, and the benefits of collaborative semantic networks will motivate people to register resource labels and publish resource descriptions on the semantic web. The Domain Ontology Oriented Resource System (DOORS) and Problem Oriented Registry of Tags and Labels (PORTAL) are proposed as infrastructure systems for resource metadata within a paradigm that can serve as a bridge between the original web and the semantic web. The Internet Registry Information Service (IRIS) registers [corrected] domain names while DNS publishes domain addresses with mapping of names to addresses for the original web. Analogously, PORTAL registers resource labels and tags while DOORS publishes resource locations and descriptions with mapping of labels to locations for the semantic web. BioPORT is proposed as a prototype PORTAL registry specific for the problem domain of biomedical computing.

HCLS 2.0/3.0: health care and life sciences data mashup using Web 2.0/3.0.

PubMed

Cheung, Kei-Hoi; Yip, Kevin Y; Townsend, Jeffrey P; Scotch, Matthew

2008-10-01

We describe the potential of current Web 2.0 technologies to achieve data mashup in the health care and life sciences (HCLS) domains, and compare that potential to the nascent trend of performing semantic mashup. After providing an overview of Web 2.0, we demonstrate two scenarios of data mashup, facilitated by the following Web 2.0 tools and sites: Yahoo! Pipes, Dapper, Google Maps and GeoCommons. In the first scenario, we exploited Dapper and Yahoo! Pipes to implement a challenging data integration task in the context of DNA microarray research. In the second scenario, we exploited Yahoo! Pipes, Google Maps, and GeoCommons to create a geographic information system (GIS) interface that allows visualization and integration of diverse categories of public health data, including cancer incidence and pollution prevalence data. Based on these two scenarios, we discuss the strengths and weaknesses of these Web 2.0 mashup technologies. We then describe Semantic Web, the mainstream Web 3.0 technology that enables more powerful data integration over the Web. We discuss the areas of intersection of Web 2.0 and Semantic Web, and describe the potential benefits that can be brought to HCLS research by combining these two sets of technologies.

HCLS 2.0/3.0: Health Care and Life Sciences Data Mashup Using Web 2.0/3.0

PubMed Central

Cheung, Kei-Hoi; Yip, Kevin Y.; Townsend, Jeffrey P.; Scotch, Matthew

2010-01-01

We describe the potential of current Web 2.0 technologies to achieve data mashup in the health care and life sciences (HCLS) domains, and compare that potential to the nascent trend of performing semantic mashup. After providing an overview of Web 2.0, we demonstrate two scenarios of data mashup, facilitated by the following Web 2.0 tools and sites: Yahoo! Pipes, Dapper, Google Maps and GeoCommons. In the first scenario, we exploited Dapper and Yahoo! Pipes to implement a challenging data integration task in the context of DNA microarray research. In the second scenario, we exploited Yahoo! Pipes, Google Maps, and GeoCommons to create a geographic information system (GIS) interface that allows visualization and integration of diverse categories of public health data, including cancer incidence and pollution prevalence data. Based on these two scenarios, we discuss the strengths and weaknesses of these Web 2.0 mashup technologies. We then describe Semantic Web, the mainstream Web 3.0 technology that enables more powerful data integration over the Web. We discuss the areas of intersection of Web 2.0 and Semantic Web, and describe the potential benefits that can be brought to HCLS research by combining these two sets of technologies. PMID:18487092

Representations for Semantic Learning Webs: Semantic Web Technology in Learning Support

ERIC Educational Resources Information Center

Dzbor, M.; Stutt, A.; Motta, E.; Collins, T.

2007-01-01

Recent work on applying semantic technologies to learning has concentrated on providing novel means of accessing and making use of learning objects. However, this is unnecessarily limiting: semantic technologies will make it possible to develop a range of educational Semantic Web services, such as interpretation, structure-visualization, support…

Biomedical semantics in the Semantic Web

PubMed Central

2011-01-01

The Semantic Web offers an ideal platform for representing and linking biomedical information, which is a prerequisite for the development and application of analytical tools to address problems in data-intensive areas such as systems biology and translational medicine. As for any new paradigm, the adoption of the Semantic Web offers opportunities and poses questions and challenges to the life sciences scientific community: which technologies in the Semantic Web stack will be more beneficial for the life sciences? Is biomedical information too complex to benefit from simple interlinked representations? What are the implications of adopting a new paradigm for knowledge representation? What are the incentives for the adoption of the Semantic Web, and who are the facilitators? Is there going to be a Semantic Web revolution in the life sciences? We report here a few reflections on these questions, following discussions at the SWAT4LS (Semantic Web Applications and Tools for Life Sciences) workshop series, of which this Journal of Biomedical Semantics special issue presents selected papers from the 2009 edition, held in Amsterdam on November 20th. PMID:21388570

Biomedical semantics in the Semantic Web.

PubMed

Splendiani, Andrea; Burger, Albert; Paschke, Adrian; Romano, Paolo; Marshall, M Scott

2011-03-07

The Semantic Web offers an ideal platform for representing and linking biomedical information, which is a prerequisite for the development and application of analytical tools to address problems in data-intensive areas such as systems biology and translational medicine. As for any new paradigm, the adoption of the Semantic Web offers opportunities and poses questions and challenges to the life sciences scientific community: which technologies in the Semantic Web stack will be more beneficial for the life sciences? Is biomedical information too complex to benefit from simple interlinked representations? What are the implications of adopting a new paradigm for knowledge representation? What are the incentives for the adoption of the Semantic Web, and who are the facilitators? Is there going to be a Semantic Web revolution in the life sciences?We report here a few reflections on these questions, following discussions at the SWAT4LS (Semantic Web Applications and Tools for Life Sciences) workshop series, of which this Journal of Biomedical Semantics special issue presents selected papers from the 2009 edition, held in Amsterdam on November 20th.

Storage and Retrieval of Large RDF Graph Using Hadoop and MapReduce

NASA Astrophysics Data System (ADS)

Farhan Husain, Mohammad; Doshi, Pankil; Khan, Latifur; Thuraisingham, Bhavani

Handling huge amount of data scalably is a matter of concern for a long time. Same is true for semantic web data. Current semantic web frameworks lack this ability. In this paper, we describe a framework that we built using Hadoop to store and retrieve large number of RDF triples. We describe our schema to store RDF data in Hadoop Distribute File System. We also present our algorithms to answer a SPARQL query. We make use of Hadoop's MapReduce framework to actually answer the queries. Our results reveal that we can store huge amount of semantic web data in Hadoop clusters built mostly by cheap commodity class hardware and still can answer queries fast enough. We conclude that ours is a scalable framework, able to handle large amount of RDF data efficiently.

Trust estimation of the semantic web using semantic web clustering

NASA Astrophysics Data System (ADS)

Shirgahi, Hossein; Mohsenzadeh, Mehran; Haj Seyyed Javadi, Hamid

2017-05-01

Development of semantic web and social network is undeniable in the Internet world these days. Widespread nature of semantic web has been very challenging to assess the trust in this field. In recent years, extensive researches have been done to estimate the trust of semantic web. Since trust of semantic web is a multidimensional problem, in this paper, we used parameters of social network authority, the value of pages links authority and semantic authority to assess the trust. Due to the large space of semantic network, we considered the problem scope to the clusters of semantic subnetworks and obtained the trust of each cluster elements as local and calculated the trust of outside resources according to their local trusts and trust of clusters to each other. According to the experimental result, the proposed method shows more than 79% Fscore that is about 11.9% in average more than Eigen, Tidal and centralised trust methods. Mean of error in this proposed method is 12.936, that is 9.75% in average less than Eigen and Tidal trust methods.

Querying phenotype-genotype relationships on patient datasets using semantic web technology: the example of Cerebrotendinous xanthomatosis.

PubMed

Taboada, María; Martínez, Diego; Pilo, Belén; Jiménez-Escrig, Adriano; Robinson, Peter N; Sobrido, María J

2012-07-31

Semantic Web technology can considerably catalyze translational genetics and genomics research in medicine, where the interchange of information between basic research and clinical levels becomes crucial. This exchange involves mapping abstract phenotype descriptions from research resources, such as knowledge databases and catalogs, to unstructured datasets produced through experimental methods and clinical practice. This is especially true for the construction of mutation databases. This paper presents a way of harmonizing abstract phenotype descriptions with patient data from clinical practice, and querying this dataset about relationships between phenotypes and genetic variants, at different levels of abstraction. Due to the current availability of ontological and terminological resources that have already reached some consensus in biomedicine, a reuse-based ontology engineering approach was followed. The proposed approach uses the Ontology Web Language (OWL) to represent the phenotype ontology and the patient model, the Semantic Web Rule Language (SWRL) to bridge the gap between phenotype descriptions and clinical data, and the Semantic Query Web Rule Language (SQWRL) to query relevant phenotype-genotype bidirectional relationships. The work tests the use of semantic web technology in the biomedical research domain named cerebrotendinous xanthomatosis (CTX), using a real dataset and ontologies. A framework to query relevant phenotype-genotype bidirectional relationships is provided. Phenotype descriptions and patient data were harmonized by defining 28 Horn-like rules in terms of the OWL concepts. In total, 24 patterns of SWQRL queries were designed following the initial list of competency questions. As the approach is based on OWL, the semantic of the framework adapts the standard logical model of an open world assumption. This work demonstrates how semantic web technologies can be used to support flexible representation and computational inference mechanisms required to query patient datasets at different levels of abstraction. The open world assumption is especially good for describing only partially known phenotype-genotype relationships, in a way that is easily extensible. In future, this type of approach could offer researchers a valuable resource to infer new data from patient data for statistical analysis in translational research. In conclusion, phenotype description formalization and mapping to clinical data are two key elements for interchanging knowledge between basic and clinical research.

Putting semantics into the semantic web: how well can it capture biology?

PubMed

Kazic, Toni

2006-01-01

Could the Semantic Web work for computations of biological interest in the way it's intended to work for movie reviews and commercial transactions? It would be wonderful if it could, so it's worth looking to see if its infrastructure is adequate to the job. The technologies of the Semantic Web make several crucial assumptions. I examine those assumptions; argue that they create significant problems; and suggest some alternative ways of achieving the Semantic Web's goals for biology.

Socio-contextual Network Mining for User Assistance in Web-based Knowledge Gathering Tasks

NASA Astrophysics Data System (ADS)

Rajendran, Balaji; Kombiah, Iyakutti

Web-based Knowledge Gathering (WKG) is a specialized and complex information seeking task carried out by many users on the web, for their various learning, and decision-making requirements. We construct a contextual semantic structure by observing the actions of the users involved in WKG task, in order to gain an understanding of their task and requirement. We also build a knowledge warehouse in the form of a master Semantic Link Network (SLX) that accommodates and assimilates all the contextual semantic structures. This master SLX, which is a socio-contextual network, is then mined to provide contextual inputs to the current users through their agents. We validated our approach through experiments and analyzed the benefits to the users in terms of resource explorations and the time saved. The results are positive enough to motivate us to implement in a larger scale.

Exploiting Recurring Structure in a Semantic Network

NASA Technical Reports Server (NTRS)

Wolfe, Shawn R.; Keller, Richard M.

2004-01-01

With the growing popularity of the Semantic Web, an increasing amount of information is becoming available in machine interpretable, semantically structured networks. Within these semantic networks are recurring structures that could be mined by existing or novel knowledge discovery methods. The mining of these semantic structures represents an interesting area that focuses on mining both for and from the Semantic Web, with surprising applicability to problems confronting the developers of Semantic Web applications. In this paper, we present representative examples of recurring structures and show how these structures could be used to increase the utility of a semantic repository deployed at NASA.

The Next G Web: Discernment, Meaning-Making, and the Implications of Web 3.0 for Education

ERIC Educational Resources Information Center

Poore, Megan

2014-01-01

What might Web 3.0 mean for education--that is, education seen as an intellectual and philosophical endeavour where we seek to critique the world and understand our place in it with others? In this paper, I argue that current emphases on the semantic functionality of Web 3.0 have the potential to concomitantly challenge and extend the humanist…

Semantic SenseLab: implementing the vision of the Semantic Web in neuroscience

PubMed Central

Samwald, Matthias; Chen, Huajun; Ruttenberg, Alan; Lim, Ernest; Marenco, Luis; Miller, Perry; Shepherd, Gordon; Cheung, Kei-Hoi

2011-01-01

Summary Objective Integrative neuroscience research needs a scalable informatics framework that enables semantic integration of diverse types of neuroscience data. This paper describes the use of the Web Ontology Language (OWL) and other Semantic Web technologies for the representation and integration of molecular-level data provided by several of SenseLab suite of neuroscience databases. Methods Based on the original database structure, we semi-automatically translated the databases into OWL ontologies with manual addition of semantic enrichment. The SenseLab ontologies are extensively linked to other biomedical Semantic Web resources, including the Subcellular Anatomy Ontology, Brain Architecture Management System, the Gene Ontology, BIRNLex and UniProt. The SenseLab ontologies have also been mapped to the Basic Formal Ontology and Relation Ontology, which helps ease interoperability with many other existing and future biomedical ontologies for the Semantic Web. In addition, approaches to representing contradictory research statements are described. The SenseLab ontologies are designed for use on the Semantic Web that enables their integration into a growing collection of biomedical information resources. Conclusion We demonstrate that our approach can yield significant potential benefits and that the Semantic Web is rapidly becoming mature enough to realize its anticipated promises. The ontologies are available online at http://neuroweb.med.yale.edu/senselab/ PMID:20006477

Semantic SenseLab: Implementing the vision of the Semantic Web in neuroscience.

PubMed

Samwald, Matthias; Chen, Huajun; Ruttenberg, Alan; Lim, Ernest; Marenco, Luis; Miller, Perry; Shepherd, Gordon; Cheung, Kei-Hoi

2010-01-01

Integrative neuroscience research needs a scalable informatics framework that enables semantic integration of diverse types of neuroscience data. This paper describes the use of the Web Ontology Language (OWL) and other Semantic Web technologies for the representation and integration of molecular-level data provided by several of SenseLab suite of neuroscience databases. Based on the original database structure, we semi-automatically translated the databases into OWL ontologies with manual addition of semantic enrichment. The SenseLab ontologies are extensively linked to other biomedical Semantic Web resources, including the Subcellular Anatomy Ontology, Brain Architecture Management System, the Gene Ontology, BIRNLex and UniProt. The SenseLab ontologies have also been mapped to the Basic Formal Ontology and Relation Ontology, which helps ease interoperability with many other existing and future biomedical ontologies for the Semantic Web. In addition, approaches to representing contradictory research statements are described. The SenseLab ontologies are designed for use on the Semantic Web that enables their integration into a growing collection of biomedical information resources. We demonstrate that our approach can yield significant potential benefits and that the Semantic Web is rapidly becoming mature enough to realize its anticipated promises. The ontologies are available online at http://neuroweb.med.yale.edu/senselab/. 2009 Elsevier B.V. All rights reserved.

Web 3.0: Implications for Online Learning

ERIC Educational Resources Information Center

Morris, Robin D.

2010-01-01

The impact of Web 3.0, also known as the Semantic Web, on online learning is yet to be determined as the Semantic Web and its technologies continue to develop. Online instructors must have a rudimentary understanding of Web 3.0 to prepare for the next phase of online learning. This paper provides an understandable definition of the Semantic Web…

A Software Engineering Approach based on WebML and BPMN to the Mediation Scenario of the SWS Challenge

NASA Astrophysics Data System (ADS)

Brambilla, Marco; Ceri, Stefano; Valle, Emanuele Della; Facca, Federico M.; Tziviskou, Christina

Although Semantic Web Services are expected to produce a revolution in the development of Web-based systems, very few enterprise-wide design experiences are available; one of the main reasons is the lack of sound Software Engineering methods and tools for the deployment of Semantic Web applications. In this chapter, we present an approach to software development for the Semantic Web based on classical Software Engineering methods (i.e., formal business process development, computer-aided and component-based software design, and automatic code generation) and on semantic methods and tools (i.e., ontology engineering, semantic service annotation and discovery).

Similarity Based Semantic Web Service Match

NASA Astrophysics Data System (ADS)

Peng, Hui; Niu, Wenjia; Huang, Ronghuai

Semantic web service discovery aims at returning the most matching advertised services to the service requester by comparing the semantic of the request service with an advertised service. The semantic of a web service are described in terms of inputs, outputs, preconditions and results in Ontology Web Language for Service (OWL-S) which formalized by W3C. In this paper we proposed an algorithm to calculate the semantic similarity of two services by weighted averaging their inputs and outputs similarities. Case study and applications show the effectiveness of our algorithm in service match.

The SWAN Scientific Discourse Ontology

PubMed Central

Ciccarese, Paolo; Wu, Elizabeth; Kinoshita, June; Wong, Gwendolyn T.; Ocana, Marco; Ruttenberg, Alan

2015-01-01

SWAN (Semantic Web Application in Neuromedicine) is a project to construct a semantically-organized, community-curated, distributed knowledge base of Theory, Evidence, and Discussion in biomedicine. Unlike Wikipedia and similar approaches, SWAN’s ontology is designed to represent and foreground both harmonizing and contradictory assertions within the total community discourse. Releases of the software, content and ontology will be initially by and for the Alzheimer Disease (AD) research community, with the obvious potential for extension into other disease research areas. The Alzheimer Research Forum, a 4,000-member web community for AD researchers, will host SWAN’s initial public release, currently scheduled for late 2007. This paper presents the current version of SWAN’s ontology of scientific discourse and presents our current thinking about its evolution including extensions and alignment with related communities, projects and ontologies. PMID:18583197

Semantic web for integrated network analysis in biomedicine.

PubMed

Chen, Huajun; Ding, Li; Wu, Zhaohui; Yu, Tong; Dhanapalan, Lavanya; Chen, Jake Y

2009-03-01

The Semantic Web technology enables integration of heterogeneous data on the World Wide Web by making the semantics of data explicit through formal ontologies. In this article, we survey the feasibility and state of the art of utilizing the Semantic Web technology to represent, integrate and analyze the knowledge in various biomedical networks. We introduce a new conceptual framework, semantic graph mining, to enable researchers to integrate graph mining with ontology reasoning in network data analysis. Through four case studies, we demonstrate how semantic graph mining can be applied to the analysis of disease-causal genes, Gene Ontology category cross-talks, drug efficacy analysis and herb-drug interactions analysis.

SoyBase Simple Semantic Web Architecture and Protocol (SSWAP) Services

USDA-ARS?s Scientific Manuscript database

Semantic web technologies offer the potential to link internet resources and data by shared concepts without having to rely on absolute lexical matches. Thus two web sites or web resources which are concerned with similar data types could be identified based on similar semantics. In the biological...

Modeling and formal representation of geospatial knowledge for the Geospatial Semantic Web

NASA Astrophysics Data System (ADS)

Huang, Hong; Gong, Jianya

2008-12-01

GML can only achieve geospatial interoperation at syntactic level. However, it is necessary to resolve difference of spatial cognition in the first place in most occasions, so ontology was introduced to describe geospatial information and services. But it is obviously difficult and improper to let users to find, match and compose services, especially in some occasions there are complicated business logics. Currently, with the gradual introduction of Semantic Web technology (e.g., OWL, SWRL), the focus of the interoperation of geospatial information has shifted from syntactic level to Semantic and even automatic, intelligent level. In this way, Geospatial Semantic Web (GSM) can be put forward as an augmentation to the Semantic Web that additionally includes geospatial abstractions as well as related reasoning, representation and query mechanisms. To advance the implementation of GSM, we first attempt to construct the mechanism of modeling and formal representation of geospatial knowledge, which are also two mostly foundational phases in knowledge engineering (KE). Our attitude in this paper is quite pragmatical: we argue that geospatial context is a formal model of the discriminate environment characters of geospatial knowledge, and the derivation, understanding and using of geospatial knowledge are located in geospatial context. Therefore, first, we put forward a primitive hierarchy of geospatial knowledge referencing first order logic, formal ontologies, rules and GML. Second, a metamodel of geospatial context is proposed and we use the modeling methods and representation languages of formal ontologies to process geospatial context. Thirdly, we extend Web Process Service (WPS) to be compatible with local DLL for geoprocessing and possess inference capability based on OWL.

Porting Social Media Contributions with SIOC

NASA Astrophysics Data System (ADS)

Bojars, Uldis; Breslin, John G.; Decker, Stefan

Social media sites, including social networking sites, have captured the attention of millions of users as well as billions of dollars in investment and acquisition. To better enable a user's access to multiple sites, portability between social media sites is required in terms of both (1) the personal profiles and friend networks and (2) a user's content objects expressed on each site. This requires representation mechanisms to interconnect both people and objects on the Web in an interoperable, extensible way. The Semantic Web provides the required representation mechanisms for portability between social media sites: it links people and objects to record and represent the heterogeneous ties that bind each to the other. The FOAF (Friend-of-a-Friend) initiative provides a solution to the first requirement, and this paper discusses how the SIOC (Semantically-Interlinked Online Communities) project can address the latter. By using agreed-upon Semantic Web formats like FOAF and SIOC to describe people, content objects, and the connections that bind them together, social media sites can interoperate and provide portable data by appealing to some common semantics. In this paper, we will discuss the application of Semantic Web technology to enhance current social media sites with semantics and to address issues with portability between social media sites. It has been shown that social media sites can serve as rich data sources for SIOC-based applications such as the SIOC Browser, but in the other direction, we will now show how SIOC data can be used to represent and port the diverse social media contributions (SMCs) made by users on heterogeneous sites.

Linked data scientometrics in semantic e-Science

NASA Astrophysics Data System (ADS)

Narock, Tom; Wimmer, Hayden

2017-03-01

The Semantic Web is inherently multi-disciplinary and many domains have taken advantage of semantic technologies. Yet, the geosciences are one of the fields leading the way in Semantic Web adoption and validation. Astronomy, Earth science, hydrology, and solar-terrestrial physics have seen a noteworthy amount of semantic integration. The geoscience community has been willing early adopters of semantic technologies and have provided essential feedback to the broader semantic web community. Yet, there has been no systematic study of the community as a whole and there exists no quantitative data on the impact and status of semantic technologies in the geosciences. We explore the applicability of Linked Data to scientometrics in the geosciences. In doing so, we gain an initial understanding of the breadth and depth of the Semantic Web in the geosciences. We identify what appears to be a transitionary period in the applicability of these technologies.

Integrating semantic web technologies and geospatial catalog services for geospatial information discovery and processing in cyberinfrastructure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yue, Peng; Gong, Jianya; Di, Liping

Abstract A geospatial catalogue service provides a network-based meta-information repository and interface for advertising and discovering shared geospatial data and services. Descriptive information (i.e., metadata) for geospatial data and services is structured and organized in catalogue services. The approaches currently available for searching and using that information are often inadequate. Semantic Web technologies show promise for better discovery methods by exploiting the underlying semantics. Such development needs special attention from the Cyberinfrastructure perspective, so that the traditional focus on discovery of and access to geospatial data can be expanded to support the increased demand for processing of geospatial information andmore » discovery of knowledge. Semantic descriptions for geospatial data, services, and geoprocessing service chains are structured, organized, and registered through extending elements in the ebXML Registry Information Model (ebRIM) of a geospatial catalogue service, which follows the interface specifications of the Open Geospatial Consortium (OGC) Catalogue Services for the Web (CSW). The process models for geoprocessing service chains, as a type of geospatial knowledge, are captured, registered, and discoverable. Semantics-enhanced discovery for geospatial data, services/service chains, and process models is described. Semantic search middleware that can support virtual data product materialization is developed for the geospatial catalogue service. The creation of such a semantics-enhanced geospatial catalogue service is important in meeting the demands for geospatial information discovery and analysis in Cyberinfrastructure.« less

The BiSciCol Triplifier: bringing biodiversity data to the Semantic Web.

PubMed

Stucky, Brian J; Deck, John; Conlin, Tom; Ziemba, Lukasz; Cellinese, Nico; Guralnick, Robert

2014-07-29

Recent years have brought great progress in efforts to digitize the world's biodiversity data, but integrating data from many different providers, and across research domains, remains challenging. Semantic Web technologies have been widely recognized by biodiversity scientists for their potential to help solve this problem, yet these technologies have so far seen little use for biodiversity data. Such slow uptake has been due, in part, to the relative complexity of Semantic Web technologies along with a lack of domain-specific software tools to help non-experts publish their data to the Semantic Web. The BiSciCol Triplifier is new software that greatly simplifies the process of converting biodiversity data in standard, tabular formats, such as Darwin Core-Archives, into Semantic Web-ready Resource Description Framework (RDF) representations. The Triplifier uses a vocabulary based on the popular Darwin Core standard, includes both Web-based and command-line interfaces, and is fully open-source software. Unlike most other RDF conversion tools, the Triplifier does not require detailed familiarity with core Semantic Web technologies, and it is tailored to a widely popular biodiversity data format and vocabulary standard. As a result, the Triplifier can often fully automate the conversion of biodiversity data to RDF, thereby making the Semantic Web much more accessible to biodiversity scientists who might otherwise have relatively little knowledge of Semantic Web technologies. Easy availability of biodiversity data as RDF will allow researchers to combine data from disparate sources and analyze them with powerful linked data querying tools. However, before software like the Triplifier, and Semantic Web technologies in general, can reach their full potential for biodiversity science, the biodiversity informatics community must address several critical challenges, such as the widespread failure to use robust, globally unique identifiers for biodiversity data.

Knowledge representation and management: towards an integration of a semantic web in daily health practice.

PubMed

Griffon, N; Charlet, J; Darmoni, Sj

2013-01-01

To summarize the best papers in the field of Knowledge Representation and Management (KRM). A synopsis of the four selected articles for the IMIA Yearbook 2013 KRM section is provided, as well as highlights of current KRM trends, in particular, of the semantic web in daily health practice. The manual selection was performed in three stages: first a set of 3,106 articles, then a second set of 86 articles followed by a third set of 15 articles, and finally the last set of four chosen articles. Among the four selected articles (see Table 1), one focuses on knowledge engineering to prevent adverse drug events; the objective of the second is to propose mappings between clinical archetypes and SNOMED CT in the context of clinical practice; the third presents an ontology to create a question-answering system; the fourth describes a biomonitoring network based on semantic web technologies. These four articles clearly indicate that the health semantic web has become a part of daily practice of health professionals since 2012. In the review of the second set of 86 articles, the same topics included in the previous IMIA yearbook remain active research fields: Knowledge extraction, automatic indexing, information retrieval, natural language processing, management of health terminologies and ontologies.

Semantic Desktop

NASA Astrophysics Data System (ADS)

Sauermann, Leo; Kiesel, Malte; Schumacher, Kinga; Bernardi, Ansgar

In diesem Beitrag wird gezeigt, wie der Arbeitsplatz der Zukunft aussehen könnte und wo das Semantic Web neue Möglichkeiten eröffnet. Dazu werden Ansätze aus dem Bereich Semantic Web, Knowledge Representation, Desktop-Anwendungen und Visualisierung vorgestellt, die es uns ermöglichen, die bestehenden Daten eines Benutzers neu zu interpretieren und zu verwenden. Dabei bringt die Kombination von Semantic Web und Desktop Computern besondere Vorteile - ein Paradigma, das unter dem Titel Semantic Desktop bekannt ist. Die beschriebenen Möglichkeiten der Applikationsintegration sind aber nicht auf den Desktop beschränkt, sondern können genauso in Web-Anwendungen Verwendung finden.

SPARQLGraph: a web-based platform for graphically querying biological Semantic Web databases.

PubMed

Schweiger, Dominik; Trajanoski, Zlatko; Pabinger, Stephan

2014-08-15

Semantic Web has established itself as a framework for using and sharing data across applications and database boundaries. Here, we present a web-based platform for querying biological Semantic Web databases in a graphical way. SPARQLGraph offers an intuitive drag & drop query builder, which converts the visual graph into a query and executes it on a public endpoint. The tool integrates several publicly available Semantic Web databases, including the databases of the just recently released EBI RDF platform. Furthermore, it provides several predefined template queries for answering biological questions. Users can easily create and save new query graphs, which can also be shared with other researchers. This new graphical way of creating queries for biological Semantic Web databases considerably facilitates usability as it removes the requirement of knowing specific query languages and database structures. The system is freely available at http://sparqlgraph.i-med.ac.at.

Publication, discovery and interoperability of Clinical Decision Support Systems: A Linked Data approach.

PubMed

Marco-Ruiz, Luis; Pedrinaci, Carlos; Maldonado, J A; Panziera, Luca; Chen, Rong; Bellika, J Gustav

2016-08-01

The high costs involved in the development of Clinical Decision Support Systems (CDSS) make it necessary to share their functionality across different systems and organizations. Service Oriented Architectures (SOA) have been proposed to allow reusing CDSS by encapsulating them in a Web service. However, strong barriers in sharing CDS functionality are still present as a consequence of lack of expressiveness of services' interfaces. Linked Services are the evolution of the Semantic Web Services paradigm to process Linked Data. They aim to provide semantic descriptions over SOA implementations to overcome the limitations derived from the syntactic nature of Web services technologies. To facilitate the publication, discovery and interoperability of CDS services by evolving them into Linked Services that expose their interfaces as Linked Data. We developed methods and models to enhance CDS SOA as Linked Services that define a rich semantic layer based on machine interpretable ontologies that powers their interoperability and reuse. These ontologies provided unambiguous descriptions of CDS services properties to expose them to the Web of Data. We developed models compliant with Linked Data principles to create a semantic representation of the components that compose CDS services. To evaluate our approach we implemented a set of CDS Linked Services using a Web service definition ontology. The definitions of Web services were linked to the models developed in order to attach unambiguous semantics to the service components. All models were bound to SNOMED-CT and public ontologies (e.g. Dublin Core) in order to count on a lingua franca to explore them. Discovery and analysis of CDS services based on machine interpretable models was performed reasoning over the ontologies built. Linked Services can be used effectively to expose CDS services to the Web of Data by building on current CDS standards. This allows building shared Linked Knowledge Bases to provide machine interpretable semantics to the CDS service description alleviating the challenges on interoperability and reuse. Linked Services allow for building 'digital libraries' of distributed CDS services that can be hosted and maintained in different organizations. Copyright © 2016 Elsevier Inc. All rights reserved.

The Semantic Web and Educational Technology

ERIC Educational Resources Information Center

Maddux, Cleborne D., Ed.

2008-01-01

The "Semantic Web" is an idea proposed by Tim Berners-Lee, the inventor of the "World Wide Web." The topic has been generating a great deal of interest and enthusiasm, and there is a rapidly growing body of literature dealing with it. This article attempts to explain how the Semantic Web would work, and explores short-term and long-term…

Querying phenotype-genotype relationships on patient datasets using semantic web technology: the example of cerebrotendinous xanthomatosis

PubMed Central

2012-01-01

Background Semantic Web technology can considerably catalyze translational genetics and genomics research in medicine, where the interchange of information between basic research and clinical levels becomes crucial. This exchange involves mapping abstract phenotype descriptions from research resources, such as knowledge databases and catalogs, to unstructured datasets produced through experimental methods and clinical practice. This is especially true for the construction of mutation databases. This paper presents a way of harmonizing abstract phenotype descriptions with patient data from clinical practice, and querying this dataset about relationships between phenotypes and genetic variants, at different levels of abstraction. Methods Due to the current availability of ontological and terminological resources that have already reached some consensus in biomedicine, a reuse-based ontology engineering approach was followed. The proposed approach uses the Ontology Web Language (OWL) to represent the phenotype ontology and the patient model, the Semantic Web Rule Language (SWRL) to bridge the gap between phenotype descriptions and clinical data, and the Semantic Query Web Rule Language (SQWRL) to query relevant phenotype-genotype bidirectional relationships. The work tests the use of semantic web technology in the biomedical research domain named cerebrotendinous xanthomatosis (CTX), using a real dataset and ontologies. Results A framework to query relevant phenotype-genotype bidirectional relationships is provided. Phenotype descriptions and patient data were harmonized by defining 28 Horn-like rules in terms of the OWL concepts. In total, 24 patterns of SWQRL queries were designed following the initial list of competency questions. As the approach is based on OWL, the semantic of the framework adapts the standard logical model of an open world assumption. Conclusions This work demonstrates how semantic web technologies can be used to support flexible representation and computational inference mechanisms required to query patient datasets at different levels of abstraction. The open world assumption is especially good for describing only partially known phenotype-genotype relationships, in a way that is easily extensible. In future, this type of approach could offer researchers a valuable resource to infer new data from patient data for statistical analysis in translational research. In conclusion, phenotype description formalization and mapping to clinical data are two key elements for interchanging knowledge between basic and clinical research. PMID:22849591

Enrichment and Ranking of the YouTube Tag Space and Integration with the Linked Data Cloud

NASA Astrophysics Data System (ADS)

Choudhury, Smitashree; Breslin, John G.; Passant, Alexandre

The increase of personal digital cameras with video functionality and video-enabled camera phones has increased the amount of user-generated videos on the Web. People are spending more and more time viewing online videos as a major source of entertainment and "infotainment". Social websites allow users to assign shared free-form tags to user-generated multimedia resources, thus generating annotations for objects with a minimum amount of effort. Tagging allows communities to organise their multimedia items into browseable sets, but these tags may be poorly chosen and related tags may be omitted. Current techniques to retrieve, integrate and present this media to users are deficient and could do with improvement. In this paper, we describe a framework for semantic enrichment, ranking and integration of web video tags using Semantic Web technologies. Semantic enrichment of folksonomies can bridge the gap between the uncontrolled and flat structures typically found in user-generated content and structures provided by the Semantic Web. The enhancement of tag spaces with semantics has been accomplished through two major tasks: (1) a tag space expansion and ranking step; and (2) through concept matching and integration with the Linked Data cloud. We have explored social, temporal and spatial contexts to enrich and extend the existing tag space. The resulting semantic tag space is modelled via a local graph based on co-occurrence distances for ranking. A ranked tag list is mapped and integrated with the Linked Data cloud through the DBpedia resource repository. Multi-dimensional context filtering for tag expansion means that tag ranking is much easier and it provides less ambiguous tag to concept matching.

Towards a semantic medical Web: HealthCyberMap's tool for building an RDF metadata base of health information resources based on the Qualified Dublin Core Metadata Set.

PubMed

Boulos, Maged N; Roudsari, Abdul V; Carson, Ewart R

2002-07-01

HealthCyberMap (http://healthcybermap.semanticweb.org/) aims at mapping Internet health information resources in novel ways for enhanced retrieval and navigation. This is achieved by collecting appropriate resource metadata in an unambiguous form that preserves semantics. We modelled a qualified Dublin Core (DC) metadata set ontology with extra elements for resource quality and geographical provenance in Prot g -2000. A metadata collection form helps acquiring resource instance data within Prot g . The DC subject field is populated with UMLS terms directly imported from UMLS Knowledge Source Server using UMLS tab, a Prot g -2000 plug-in. The project is saved in RDFS/RDF. The ontology and associated form serve as a free tool for building and maintaining an RDF medical resource metadata base. The UMLS tab enables browsing and searching for concepts that best describe a resource, and importing them to DC subject fields. The resultant metadata base can be used with a search and inference engine, and have textual and/or visual navigation interface(s) applied to it, to ultimately build a medical Semantic Web portal. Different ways of exploiting Prot g -2000 RDF output are discussed. By making the context and semantics of resources, not merely their raw text and formatting, amenable to computer 'understanding,' we can build a Semantic Web that is more useful to humans than the current Web. This requires proper use of metadata and ontologies. Clinical codes can reliably describe the subjects of medical resources, establish the semantic relationships (as defined by underlying coding scheme) between related resources, and automate their topical categorisation.

Ontology Based Quality Evaluation for Spatial Data

NASA Astrophysics Data System (ADS)

Yılmaz, C.; Cömert, Ç.

2015-08-01

Many institutions will be providing data to the National Spatial Data Infrastructure (NSDI). Current technical background of the NSDI is based on syntactic web services. It is expected that this will be replaced by semantic web services. The quality of the data provided is important in terms of the decision-making process and the accuracy of transactions. Therefore, the data quality needs to be tested. This topic has been neglected in Turkey. Data quality control for NSDI may be done by private or public "data accreditation" institutions. A methodology is required for data quality evaluation. There are studies for data quality including ISO standards, academic studies and software to evaluate spatial data quality. ISO 19157 standard defines the data quality elements. Proprietary software such as, 1Spatial's 1Validate and ESRI's Data Reviewer offers quality evaluation based on their own classification of rules. Commonly, rule based approaches are used for geospatial data quality check. In this study, we look for the technical components to devise and implement a rule based approach with ontologies using free and open source software in semantic web context. Semantic web uses ontologies to deliver well-defined web resources and make them accessible to end-users and processes. We have created an ontology conforming to the geospatial data and defined some sample rules to show how to test data with respect to data quality elements including; attribute, topo-semantic and geometrical consistency using free and open source software. To test data against rules, sample GeoSPARQL queries are created, associated with specifications.

Intelligent Learning Infrastructure for Knowledge Intensive Organizations: A Semantic Web Perspective

ERIC Educational Resources Information Center

Lytras, Miltiadis, Ed.; Naeve, Ambjorn, Ed.

2005-01-01

In the context of Knowledge Society, the convergence of knowledge and learning management is a critical milestone. "Intelligent Learning Infrastructure for Knowledge Intensive Organizations: A Semantic Web Perspective" provides state-of-the art knowledge through a balanced theoretical and technological discussion. The semantic web perspective…

Social Networking on the Semantic Web

ERIC Educational Resources Information Center

Finin, Tim; Ding, Li; Zhou, Lina; Joshi, Anupam

2005-01-01

Purpose: Aims to investigate the way that the semantic web is being used to represent and process social network information. Design/methodology/approach: The Swoogle semantic web search engine was used to construct several large data sets of Resource Description Framework (RDF) documents with social network information that were encoded using the…

CNTRO: A Semantic Web Ontology for Temporal Relation Inferencing in Clinical Narratives.

PubMed

Tao, Cui; Wei, Wei-Qi; Solbrig, Harold R; Savova, Guergana; Chute, Christopher G

2010-11-13

Using Semantic-Web specifications to represent temporal information in clinical narratives is an important step for temporal reasoning and answering time-oriented queries. Existing temporal models are either not compatible with the powerful reasoning tools developed for the Semantic Web, or designed only for structured clinical data and therefore are not ready to be applied on natural-language-based clinical narrative reports directly. We have developed a Semantic-Web ontology which is called Clinical Narrative Temporal Relation ontology. Using this ontology, temporal information in clinical narratives can be represented as RDF (Resource Description Framework) triples. More temporal information and relations can then be inferred by Semantic-Web based reasoning tools. Experimental results show that this ontology can represent temporal information in real clinical narratives successfully.

COEUS: “semantic web in a box” for biomedical applications

PubMed Central

2012-01-01

Background As the “omics” revolution unfolds, the growth in data quantity and diversity is bringing about the need for pioneering bioinformatics software, capable of significantly improving the research workflow. To cope with these computer science demands, biomedical software engineers are adopting emerging semantic web technologies that better suit the life sciences domain. The latter’s complex relationships are easily mapped into semantic web graphs, enabling a superior understanding of collected knowledge. Despite increased awareness of semantic web technologies in bioinformatics, their use is still limited. Results COEUS is a new semantic web framework, aiming at a streamlined application development cycle and following a “semantic web in a box” approach. The framework provides a single package including advanced data integration and triplification tools, base ontologies, a web-oriented engine and a flexible exploration API. Resources can be integrated from heterogeneous sources, including CSV and XML files or SQL and SPARQL query results, and mapped directly to one or more ontologies. Advanced interoperability features include REST services, a SPARQL endpoint and LinkedData publication. These enable the creation of multiple applications for web, desktop or mobile environments, and empower a new knowledge federation layer. Conclusions The platform, targeted at biomedical application developers, provides a complete skeleton ready for rapid application deployment, enhancing the creation of new semantic information systems. COEUS is available as open source at http://bioinformatics.ua.pt/coeus/. PMID:23244467

COEUS: "semantic web in a box" for biomedical applications.

PubMed

Lopes, Pedro; Oliveira, José Luís

2012-12-17

As the "omics" revolution unfolds, the growth in data quantity and diversity is bringing about the need for pioneering bioinformatics software, capable of significantly improving the research workflow. To cope with these computer science demands, biomedical software engineers are adopting emerging semantic web technologies that better suit the life sciences domain. The latter's complex relationships are easily mapped into semantic web graphs, enabling a superior understanding of collected knowledge. Despite increased awareness of semantic web technologies in bioinformatics, their use is still limited. COEUS is a new semantic web framework, aiming at a streamlined application development cycle and following a "semantic web in a box" approach. The framework provides a single package including advanced data integration and triplification tools, base ontologies, a web-oriented engine and a flexible exploration API. Resources can be integrated from heterogeneous sources, including CSV and XML files or SQL and SPARQL query results, and mapped directly to one or more ontologies. Advanced interoperability features include REST services, a SPARQL endpoint and LinkedData publication. These enable the creation of multiple applications for web, desktop or mobile environments, and empower a new knowledge federation layer. The platform, targeted at biomedical application developers, provides a complete skeleton ready for rapid application deployment, enhancing the creation of new semantic information systems. COEUS is available as open source at http://bioinformatics.ua.pt/coeus/.

A Generic Evaluation Model for Semantic Web Services

NASA Astrophysics Data System (ADS)

Shafiq, Omair

Semantic Web Services research has gained momentum over the last few Years and by now several realizations exist. They are being used in a number of industrial use-cases. Soon software developers will be expected to use this infrastructure to build their B2B applications requiring dynamic integration. However, there is still a lack of guidelines for the evaluation of tools developed to realize Semantic Web Services and applications built on top of them. In normal software engineering practice such guidelines can already be found for traditional component-based systems. Also some efforts are being made to build performance models for servicebased systems. Drawing on these related efforts in component-oriented and servicebased systems, we identified the need for a generic evaluation model for Semantic Web Services applicable to any realization. The generic evaluation model will help users and customers to orient their systems and solutions towards using Semantic Web Services. In this chapter, we have presented the requirements for the generic evaluation model for Semantic Web Services and further discussed the initial steps that we took to sketch such a model. Finally, we discuss related activities for evaluating semantic technologies.

HyQue: evaluating hypotheses using Semantic Web technologies.

PubMed

Callahan, Alison; Dumontier, Michel; Shah, Nigam H

2011-05-17

Key to the success of e-Science is the ability to computationally evaluate expert-composed hypotheses for validity against experimental data. Researchers face the challenge of collecting, evaluating and integrating large amounts of diverse information to compose and evaluate a hypothesis. Confronted with rapidly accumulating data, researchers currently do not have the software tools to undertake the required information integration tasks. We present HyQue, a Semantic Web tool for querying scientific knowledge bases with the purpose of evaluating user submitted hypotheses. HyQue features a knowledge model to accommodate diverse hypotheses structured as events and represented using Semantic Web languages (RDF/OWL). Hypothesis validity is evaluated against experimental and literature-sourced evidence through a combination of SPARQL queries and evaluation rules. Inference over OWL ontologies (for type specifications, subclass assertions and parthood relations) and retrieval of facts stored as Bio2RDF linked data provide support for a given hypothesis. We evaluate hypotheses of varying levels of detail about the genetic network controlling galactose metabolism in Saccharomyces cerevisiae to demonstrate the feasibility of deploying such semantic computing tools over a growing body of structured knowledge in Bio2RDF. HyQue is a query-based hypothesis evaluation system that can currently evaluate hypotheses about the galactose metabolism in S. cerevisiae. Hypotheses as well as the supporting or refuting data are represented in RDF and directly linked to one another allowing scientists to browse from data to hypothesis and vice versa. HyQue hypotheses and data are available at http://semanticscience.org/projects/hyque.

Information integration from heterogeneous data sources: a Semantic Web approach.

PubMed

Kunapareddy, Narendra; Mirhaji, Parsa; Richards, David; Casscells, S Ward

2006-01-01

Although the decentralized and autonomous implementation of health information systems has made it possible to extend the reach of surveillance systems to a variety of contextually disparate domains, public health use of data from these systems is not primarily anticipated. The Semantic Web has been proposed to address both representational and semantic heterogeneity in distributed and collaborative environments. We introduce a semantic approach for the integration of health data using the Resource Definition Framework (RDF) and the Simple Knowledge Organization System (SKOS) developed by the Semantic Web community.

Discovering Central Practitioners in a Medical Discussion Forum Using Semantic Web Analytics.

PubMed

Rajabi, Enayat; Abidi, Syed Sibte Raza

2017-01-01

The aim of this paper is to investigate semantic web based methods to enrich and transform a medical discussion forum in order to perform semantics-driven social network analysis. We use the centrality measures as well as semantic similarity metrics to identify the most influential practitioners within a discussion forum. The centrality results of our approach are in line with centrality measures produced by traditional SNA methods, thus validating the applicability of semantic web based methods for SNA, particularly for analyzing social networks for specialized discussion forums.

Towards a semantic PACS: Using Semantic Web technology to represent imaging data.

PubMed

Van Soest, Johan; Lustberg, Tim; Grittner, Detlef; Marshall, M Scott; Persoon, Lucas; Nijsten, Bas; Feltens, Peter; Dekker, Andre

2014-01-01

The DICOM standard is ubiquitous within medicine. However, improved DICOM semantics would significantly enhance search operations. Furthermore, databases of current PACS systems are not flexible enough for the demands within image analysis research. In this paper, we investigated if we can use Semantic Web technology, to store and represent metadata of DICOM image files, as well as linking additional computational results to image metadata. Therefore, we developed a proof of concept containing two applications: one to store commonly used DICOM metadata in an RDF repository, and one to calculate imaging biomarkers based on DICOM images, and store the biomarker values in an RDF repository. This enabled us to search for all patients with a gross tumor volume calculated to be larger than 50 cc. We have shown that we can successfully store the DICOM metadata in an RDF repository and are refining our proof of concept with regards to volume naming, value representation, and the applications themselves.

Semantic querying of relational data for clinical intelligence: a semantic web services-based approach

PubMed Central

2013-01-01

Background Clinical Intelligence, as a research and engineering discipline, is dedicated to the development of tools for data analysis for the purposes of clinical research, surveillance, and effective health care management. Self-service ad hoc querying of clinical data is one desirable type of functionality. Since most of the data are currently stored in relational or similar form, ad hoc querying is problematic as it requires specialised technical skills and the knowledge of particular data schemas. Results A possible solution is semantic querying where the user formulates queries in terms of domain ontologies that are much easier to navigate and comprehend than data schemas. In this article, we are exploring the possibility of using SADI Semantic Web services for semantic querying of clinical data. We have developed a prototype of a semantic querying infrastructure for the surveillance of, and research on, hospital-acquired infections. Conclusions Our results suggest that SADI can support ad-hoc, self-service, semantic queries of relational data in a Clinical Intelligence context. The use of SADI compares favourably with approaches based on declarative semantic mappings from data schemas to ontologies, such as query rewriting and RDFizing by materialisation, because it can easily cope with situations when (i) some computation is required to turn relational data into RDF or OWL, e.g., to implement temporal reasoning, or (ii) integration with external data sources is necessary. PMID:23497556

Semantics of data and service registration to advance interdisciplinary information and data access.

NASA Astrophysics Data System (ADS)

Fox, P. P.; McGuinness, D. L.; Raskin, R.; Sinha, A. K.

2008-12-01

In developing an application of semantic web methods and technologies to address the integration of heterogeneous and interdisciplinary earth-science datasets, we have developed methodologies for creating rich semantic descriptions (ontologies) of the application domains. We have leveraged and extended where possible existing ontology frameworks such as SWEET. As a result of this semantic approach, we have also utilized ontologic descriptions of key enabling elements of the application, such as the registration of datasets with ontologies at several levels of granularity. This has enabled the location and usage of the data across disciplines. We are also realizing the need to develop similar semantic registration of web service data holdings as well as those provided with community and/or standard markup languages (e.g. GeoSciML). This level of semantic enablement extending beyond domain terms and relations significantly enhances our ability to provide a coherent semantic data framework for data and information systems. Much of this work is on the frontier of technology development and we will present the current and near-future capabilities we are developing. This work arises from the Semantically-Enabled Science Data Integration (SESDI) project, which is an NASA/ESTO/ACCESS-funded project involving the High Altitude Observatory at the National Center for Atmospheric Research (NCAR), McGuinness Associates Consulting, NASA/JPL and Virginia Polytechnic University.

Challenges Facing the Semantic Web and Social Software as Communication Technology Agents in E-Learning Environments

ERIC Educational Resources Information Center

Olaniran, Bolanle A.

2010-01-01

The semantic web describes the process whereby information content is made available for machine consumption. With increased reliance on information communication technologies, the semantic web promises effective and efficient information acquisition and dissemination of products and services in the global economy, in particular, e-learning.…

Practical Experiences for the Development of Educational Systems in the Semantic Web

ERIC Educational Resources Information Center

Sánchez Vera, Ma. del Mar; Tomás Fernández Breis, Jesualdo; Serrano Sánchez, José Luis; Prendes Espinosa, Ma. Paz

2013-01-01

Semantic Web technologies have been applied in educational settings for different purposes in recent years, with the type of application being mainly defined by the way in which knowledge is represented and exploited. The basic technology for knowledge representation in Semantic Web settings is the ontology, which represents a common, shareable…

Comprehensive Analysis of Semantic Web Reasoners and Tools: A Survey

ERIC Educational Resources Information Center

Khamparia, Aditya; Pandey, Babita

2017-01-01

Ontologies are emerging as best representation techniques for knowledge based context domains. The continuing need for interoperation, collaboration and effective information retrieval has lead to the creation of semantic web with the help of tools and reasoners which manages personalized information. The future of semantic web lies in an ontology…

An Intelligent Semantic E-Learning Framework Using Context-Aware Semantic Web Technologies

ERIC Educational Resources Information Center

Huang, Weihong; Webster, David; Wood, Dawn; Ishaya, Tanko

2006-01-01

Recent developments of e-learning specifications such as Learning Object Metadata (LOM), Sharable Content Object Reference Model (SCORM), Learning Design and other pedagogy research in semantic e-learning have shown a trend of applying innovative computational techniques, especially Semantic Web technologies, to promote existing content-focused…

Personalization of Rule-based Web Services.

PubMed

Choi, Okkyung; Han, Sang Yong

2008-04-04

Nowadays Web users have clearly expressed their wishes to receive personalized services directly. Personalization is the way to tailor services directly to the immediate requirements of the user. However, the current Web Services System does not provide any features supporting this such as consideration of personalization of services and intelligent matchmaking. In this research a flexible, personalized Rule-based Web Services System to address these problems and to enable efficient search, discovery and construction across general Web documents and Semantic Web documents in a Web Services System is proposed. This system utilizes matchmaking among service requesters', service providers' and users' preferences using a Rule-based Search Method, and subsequently ranks search results. A prototype of efficient Web Services search and construction for the suggested system is developed based on the current work.

Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources

PubMed Central

Waagmeester, Andra; Pico, Alexander R.

2016-01-01

The diversity of online resources storing biological data in different formats provides a challenge for bioinformaticians to integrate and analyse their biological data. The semantic web provides a standard to facilitate knowledge integration using statements built as triples describing a relation between two objects. WikiPathways, an online collaborative pathway resource, is now available in the semantic web through a SPARQL endpoint at http://sparql.wikipathways.org. Having biological pathways in the semantic web allows rapid integration with data from other resources that contain information about elements present in pathways using SPARQL queries. In order to convert WikiPathways content into meaningful triples we developed two new vocabularies that capture the graphical representation and the pathway logic, respectively. Each gene, protein, and metabolite in a given pathway is defined with a standard set of identifiers to support linking to several other biological resources in the semantic web. WikiPathways triples were loaded into the Open PHACTS discovery platform and are available through its Web API (https://dev.openphacts.org/docs) to be used in various tools for drug development. We combined various semantic web resources with the newly converted WikiPathways content using a variety of SPARQL query types and third-party resources, such as the Open PHACTS API. The ability to use pathway information to form new links across diverse biological data highlights the utility of integrating WikiPathways in the semantic web. PMID:27336457

Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources.

PubMed

Waagmeester, Andra; Kutmon, Martina; Riutta, Anders; Miller, Ryan; Willighagen, Egon L; Evelo, Chris T; Pico, Alexander R

2016-06-01

The diversity of online resources storing biological data in different formats provides a challenge for bioinformaticians to integrate and analyse their biological data. The semantic web provides a standard to facilitate knowledge integration using statements built as triples describing a relation between two objects. WikiPathways, an online collaborative pathway resource, is now available in the semantic web through a SPARQL endpoint at http://sparql.wikipathways.org. Having biological pathways in the semantic web allows rapid integration with data from other resources that contain information about elements present in pathways using SPARQL queries. In order to convert WikiPathways content into meaningful triples we developed two new vocabularies that capture the graphical representation and the pathway logic, respectively. Each gene, protein, and metabolite in a given pathway is defined with a standard set of identifiers to support linking to several other biological resources in the semantic web. WikiPathways triples were loaded into the Open PHACTS discovery platform and are available through its Web API (https://dev.openphacts.org/docs) to be used in various tools for drug development. We combined various semantic web resources with the newly converted WikiPathways content using a variety of SPARQL query types and third-party resources, such as the Open PHACTS API. The ability to use pathway information to form new links across diverse biological data highlights the utility of integrating WikiPathways in the semantic web.

Pragmatic Computing - A Semiotic Perspective to Web Services

NASA Astrophysics Data System (ADS)

Liu, Kecheng

The web seems to have evolved from a syntactic web, a semantic web to a pragmatic web. This evolution conforms to the study of information and technology from the theory of semiotics. The pragmatics, concerning with the use of information in relation to the context and intended purposes, is extremely important in web service and applications. Much research in pragmatics has been carried out; but in the same time, attempts and solutions have led to some more questions. After reviewing the current work in pragmatic web, the paper presents a semiotic approach to website services, particularly on request decomposition and service aggregation.

Provenance-Based Approaches to Semantic Web Service Discovery and Usage

ERIC Educational Resources Information Center

Narock, Thomas William

2012-01-01

The World Wide Web Consortium defines a Web Service as "a software system designed to support interoperable machine-to-machine interaction over a network." Web Services have become increasingly important both within and across organizational boundaries. With the recent advent of the Semantic Web, web services have evolved into semantic…

Ontology Reuse in Geoscience Semantic Applications

NASA Astrophysics Data System (ADS)

Mayernik, M. S.; Gross, M. B.; Daniels, M. D.; Rowan, L. R.; Stott, D.; Maull, K. E.; Khan, H.; Corson-Rikert, J.

2015-12-01

The tension between local ontology development and wider ontology connections is fundamental to the Semantic web. It is often unclear, however, what the key decision points should be for new semantic web applications in deciding when to reuse existing ontologies and when to develop original ontologies. In addition, with the growth of semantic web ontologies and applications, new semantic web applications can struggle to efficiently and effectively identify and select ontologies to reuse. This presentation will describe the ontology comparison, selection, and consolidation effort within the EarthCollab project. UCAR, Cornell University, and UNAVCO are collaborating on the EarthCollab project to use semantic web technologies to enable the discovery of the research output from a diverse array of projects. The EarthCollab project is using the VIVO Semantic web software suite to increase discoverability of research information and data related to the following two geoscience-based communities: (1) the Bering Sea Project, an interdisciplinary field program whose data archive is hosted by NCAR's Earth Observing Laboratory (EOL), and (2) diverse research projects informed by geodesy through the UNAVCO geodetic facility and consortium. This presentation will outline of EarthCollab use cases, and provide an overview of key ontologies being used, including the VIVO-Integrated Semantic Framework (VIVO-ISF), Global Change Information System (GCIS), and Data Catalog (DCAT) ontologies. We will discuss issues related to bringing these ontologies together to provide a robust ontological structure to support the EarthCollab use cases. It is rare that a single pre-existing ontology meets all of a new application's needs. New projects need to stitch ontologies together in ways that fit into the broader semantic web ecosystem.

ER2OWL: Generating OWL Ontology from ER Diagram

NASA Astrophysics Data System (ADS)

Fahad, Muhammad

Ontology is the fundamental part of Semantic Web. The goal of W3C is to bring the web into (its full potential) a semantic web with reusing previous systems and artifacts. Most legacy systems have been documented in structural analysis and structured design (SASD), especially in simple or Extended ER Diagram (ERD). Such systems need up-gradation to become the part of semantic web. In this paper, we present ERD to OWL-DL ontology transformation rules at concrete level. These rules facilitate an easy and understandable transformation from ERD to OWL. The set of rules for transformation is tested on a structured analysis and design example. The framework provides OWL ontology for semantic web fundamental. This framework helps software engineers in upgrading the structured analysis and design artifact ERD, to components of semantic web. Moreover our transformation tool, ER2OWL, reduces the cost and time for building OWL ontologies with the reuse of existing entity relationship models.

NASA and The Semantic Web

NASA Technical Reports Server (NTRS)

Ashish, Naveen

2005-01-01

We provide an overview of several ongoing NASA endeavors based on concepts, systems, and technology from the Semantic Web arena. Indeed NASA has been one of the early adopters of Semantic Web Technology and we describe ongoing and completed R&D efforts for several applications ranging from collaborative systems to airspace information management to enterprise search to scientific information gathering and discovery systems at NASA.

A Research on E - learning Resources Construction Based on Semantic Web

NASA Astrophysics Data System (ADS)

Rui, Liu; Maode, Deng

Traditional e-learning platforms have the flaws that it's usually difficult to query or positioning, and realize the cross platform sharing and interoperability. In the paper, the semantic web and metadata standard is discussed, and a kind of e - learning system framework based on semantic web is put forward to try to solve the flaws of traditional elearning platforms.

F-OWL: An Inference Engine for Semantic Web

NASA Technical Reports Server (NTRS)

Zou, Youyong; Finin, Tim; Chen, Harry

2004-01-01

Understanding and using the data and knowledge encoded in semantic web documents requires an inference engine. F-OWL is an inference engine for the semantic web language OWL language based on F-logic, an approach to defining frame-based systems in logic. F-OWL is implemented using XSB and Flora-2 and takes full advantage of their features. We describe how F-OWL computes ontology entailment and compare it with other description logic based approaches. We also describe TAGA, a trading agent environment that we have used as a test bed for F-OWL and to explore how multiagent systems can use semantic web concepts and technology.

SOLE: Applying Semantics and Social Web to Support Technology Enhanced Learning in Software Engineering

NASA Astrophysics Data System (ADS)

Colomo-Palacios, Ricardo; Jiménez-López, Diego; García-Crespo, Ángel; Blanco-Iglesias, Borja

eLearning educative processes are a challenge for educative institutions and education professionals. In an environment in which learning resources are being produced, catalogued and stored using innovative ways, SOLE provides a platform in which exam questions can be produced supported by Web 2.0 tools, catalogued and labeled via semantic web and stored and distributed using eLearning standards. This paper presents, SOLE, a social network of exam questions sharing particularized for Software Engineering domain, based on semantics and built using semantic web and eLearning standards, such as IMS Question and Test Interoperability specification 2.1.

Experimenting with semantic web services to understand the role of NLP technologies in healthcare.

PubMed

Jagannathan, V

2006-01-01

NLP technologies can play a significant role in healthcare where a predominant segment of the clinical documentation is in text form. In a graduate course focused on understanding semantic web services at West Virginia University, a class project was designed with the purpose of exploring potential use for NLP-based abstraction of clinical documentation. The role of NLP-technology was simulated using human abstractors and various workflows were investigated using public domain workflow and semantic web service technologies. This poster explores the potential use of NLP and the role of workflow and semantic web technologies in developing healthcare IT environments.

Introduction to geospatial semantics and technology workshop handbook

USGS Publications Warehouse

Varanka, Dalia E.

2012-01-01

The workshop is a tutorial on introductory geospatial semantics with hands-on exercises using standard Web browsers. The workshop is divided into two sections, general semantics on the Web and specific examples of geospatial semantics using data from The National Map of the U.S. Geological Survey and the Open Ontology Repository. The general semantics section includes information and access to publicly available semantic archives. The specific session includes information on geospatial semantics with access to semantically enhanced data for hydrography, transportation, boundaries, and names. The Open Ontology Repository offers open-source ontologies for public use.

A semantic-web oriented representation of the clinical element model for secondary use of electronic health records data.

PubMed

Tao, Cui; Jiang, Guoqian; Oniki, Thomas A; Freimuth, Robert R; Zhu, Qian; Sharma, Deepak; Pathak, Jyotishman; Huff, Stanley M; Chute, Christopher G

2013-05-01

The clinical element model (CEM) is an information model designed for representing clinical information in electronic health records (EHR) systems across organizations. The current representation of CEMs does not support formal semantic definitions and therefore it is not possible to perform reasoning and consistency checking on derived models. This paper introduces our efforts to represent the CEM specification using the Web Ontology Language (OWL). The CEM-OWL representation connects the CEM content with the Semantic Web environment, which provides authoring, reasoning, and querying tools. This work may also facilitate the harmonization of the CEMs with domain knowledge represented in terminology models as well as other clinical information models such as the openEHR archetype model. We have created the CEM-OWL meta ontology based on the CEM specification. A convertor has been implemented in Java to automatically translate detailed CEMs from XML to OWL. A panel evaluation has been conducted, and the results show that the OWL modeling can faithfully represent the CEM specification and represent patient data.

A semantic-web oriented representation of the clinical element model for secondary use of electronic health records data

PubMed Central

Tao, Cui; Jiang, Guoqian; Oniki, Thomas A; Freimuth, Robert R; Zhu, Qian; Sharma, Deepak; Pathak, Jyotishman; Huff, Stanley M; Chute, Christopher G

2013-01-01

The clinical element model (CEM) is an information model designed for representing clinical information in electronic health records (EHR) systems across organizations. The current representation of CEMs does not support formal semantic definitions and therefore it is not possible to perform reasoning and consistency checking on derived models. This paper introduces our efforts to represent the CEM specification using the Web Ontology Language (OWL). The CEM-OWL representation connects the CEM content with the Semantic Web environment, which provides authoring, reasoning, and querying tools. This work may also facilitate the harmonization of the CEMs with domain knowledge represented in terminology models as well as other clinical information models such as the openEHR archetype model. We have created the CEM-OWL meta ontology based on the CEM specification. A convertor has been implemented in Java to automatically translate detailed CEMs from XML to OWL. A panel evaluation has been conducted, and the results show that the OWL modeling can faithfully represent the CEM specification and represent patient data. PMID:23268487

HyQue: evaluating hypotheses using Semantic Web technologies

PubMed Central

2011-01-01

Background Key to the success of e-Science is the ability to computationally evaluate expert-composed hypotheses for validity against experimental data. Researchers face the challenge of collecting, evaluating and integrating large amounts of diverse information to compose and evaluate a hypothesis. Confronted with rapidly accumulating data, researchers currently do not have the software tools to undertake the required information integration tasks. Results We present HyQue, a Semantic Web tool for querying scientific knowledge bases with the purpose of evaluating user submitted hypotheses. HyQue features a knowledge model to accommodate diverse hypotheses structured as events and represented using Semantic Web languages (RDF/OWL). Hypothesis validity is evaluated against experimental and literature-sourced evidence through a combination of SPARQL queries and evaluation rules. Inference over OWL ontologies (for type specifications, subclass assertions and parthood relations) and retrieval of facts stored as Bio2RDF linked data provide support for a given hypothesis. We evaluate hypotheses of varying levels of detail about the genetic network controlling galactose metabolism in Saccharomyces cerevisiae to demonstrate the feasibility of deploying such semantic computing tools over a growing body of structured knowledge in Bio2RDF. Conclusions HyQue is a query-based hypothesis evaluation system that can currently evaluate hypotheses about the galactose metabolism in S. cerevisiae. Hypotheses as well as the supporting or refuting data are represented in RDF and directly linked to one another allowing scientists to browse from data to hypothesis and vice versa. HyQue hypotheses and data are available at http://semanticscience.org/projects/hyque. PMID:21624158

The Semantic Automated Discovery and Integration (SADI) Web service Design-Pattern, API and Reference Implementation

PubMed Central

2011-01-01

Background The complexity and inter-related nature of biological data poses a difficult challenge for data and tool integration. There has been a proliferation of interoperability standards and projects over the past decade, none of which has been widely adopted by the bioinformatics community. Recent attempts have focused on the use of semantics to assist integration, and Semantic Web technologies are being welcomed by this community. Description SADI - Semantic Automated Discovery and Integration - is a lightweight set of fully standards-compliant Semantic Web service design patterns that simplify the publication of services of the type commonly found in bioinformatics and other scientific domains. Using Semantic Web technologies at every level of the Web services "stack", SADI services consume and produce instances of OWL Classes following a small number of very straightforward best-practices. In addition, we provide codebases that support these best-practices, and plug-in tools to popular developer and client software that dramatically simplify deployment of services by providers, and the discovery and utilization of those services by their consumers. Conclusions SADI Services are fully compliant with, and utilize only foundational Web standards; are simple to create and maintain for service providers; and can be discovered and utilized in a very intuitive way by biologist end-users. In addition, the SADI design patterns significantly improve the ability of software to automatically discover appropriate services based on user-needs, and automatically chain these into complex analytical workflows. We show that, when resources are exposed through SADI, data compliant with a given ontological model can be automatically gathered, or generated, from these distributed, non-coordinating resources - a behaviour we have not observed in any other Semantic system. Finally, we show that, using SADI, data dynamically generated from Web services can be explored in a manner very similar to data housed in static triple-stores, thus facilitating the intersection of Web services and Semantic Web technologies. PMID:22024447

The Semantic Automated Discovery and Integration (SADI) Web service Design-Pattern, API and Reference Implementation.

PubMed

Wilkinson, Mark D; Vandervalk, Benjamin; McCarthy, Luke

2011-10-24

The complexity and inter-related nature of biological data poses a difficult challenge for data and tool integration. There has been a proliferation of interoperability standards and projects over the past decade, none of which has been widely adopted by the bioinformatics community. Recent attempts have focused on the use of semantics to assist integration, and Semantic Web technologies are being welcomed by this community. SADI - Semantic Automated Discovery and Integration - is a lightweight set of fully standards-compliant Semantic Web service design patterns that simplify the publication of services of the type commonly found in bioinformatics and other scientific domains. Using Semantic Web technologies at every level of the Web services "stack", SADI services consume and produce instances of OWL Classes following a small number of very straightforward best-practices. In addition, we provide codebases that support these best-practices, and plug-in tools to popular developer and client software that dramatically simplify deployment of services by providers, and the discovery and utilization of those services by their consumers. SADI Services are fully compliant with, and utilize only foundational Web standards; are simple to create and maintain for service providers; and can be discovered and utilized in a very intuitive way by biologist end-users. In addition, the SADI design patterns significantly improve the ability of software to automatically discover appropriate services based on user-needs, and automatically chain these into complex analytical workflows. We show that, when resources are exposed through SADI, data compliant with a given ontological model can be automatically gathered, or generated, from these distributed, non-coordinating resources - a behaviour we have not observed in any other Semantic system. Finally, we show that, using SADI, data dynamically generated from Web services can be explored in a manner very similar to data housed in static triple-stores, thus facilitating the intersection of Web services and Semantic Web technologies.

A user-centred evaluation framework for the Sealife semantic web browsers

PubMed Central

Oliver, Helen; Diallo, Gayo; de Quincey, Ed; Alexopoulou, Dimitra; Habermann, Bianca; Kostkova, Patty; Schroeder, Michael; Jupp, Simon; Khelif, Khaled; Stevens, Robert; Jawaheer, Gawesh; Madle, Gemma

2009-01-01

Background Semantically-enriched browsing has enhanced the browsing experience by providing contextualised dynamically generated Web content, and quicker access to searched-for information. However, adoption of Semantic Web technologies is limited and user perception from the non-IT domain sceptical. Furthermore, little attention has been given to evaluating semantic browsers with real users to demonstrate the enhancements and obtain valuable feedback. The Sealife project investigates semantic browsing and its application to the life science domain. Sealife's main objective is to develop the notion of context-based information integration by extending three existing Semantic Web browsers (SWBs) to link the existing Web to the eScience infrastructure. Methods This paper describes a user-centred evaluation framework that was developed to evaluate the Sealife SWBs that elicited feedback on users' perceptions on ease of use and information findability. Three sources of data: i) web server logs; ii) user questionnaires; and iii) semi-structured interviews were analysed and comparisons made between each browser and a control system. Results It was found that the evaluation framework used successfully elicited users' perceptions of the three distinct SWBs. The results indicate that the browser with the most mature and polished interface was rated higher for usability, and semantic links were used by the users of all three browsers. Conclusion Confirmation or contradiction of our original hypotheses with relation to SWBs is detailed along with observations of implementation issues. PMID:19796398

A user-centred evaluation framework for the Sealife semantic web browsers.

PubMed

Oliver, Helen; Diallo, Gayo; de Quincey, Ed; Alexopoulou, Dimitra; Habermann, Bianca; Kostkova, Patty; Schroeder, Michael; Jupp, Simon; Khelif, Khaled; Stevens, Robert; Jawaheer, Gawesh; Madle, Gemma

2009-10-01

Semantically-enriched browsing has enhanced the browsing experience by providing contextualized dynamically generated Web content, and quicker access to searched-for information. However, adoption of Semantic Web technologies is limited and user perception from the non-IT domain sceptical. Furthermore, little attention has been given to evaluating semantic browsers with real users to demonstrate the enhancements and obtain valuable feedback. The Sealife project investigates semantic browsing and its application to the life science domain. Sealife's main objective is to develop the notion of context-based information integration by extending three existing Semantic Web browsers (SWBs) to link the existing Web to the eScience infrastructure. This paper describes a user-centred evaluation framework that was developed to evaluate the Sealife SWBs that elicited feedback on users' perceptions on ease of use and information findability. Three sources of data: i) web server logs; ii) user questionnaires; and iii) semi-structured interviews were analysed and comparisons made between each browser and a control system. It was found that the evaluation framework used successfully elicited users' perceptions of the three distinct SWBs. The results indicate that the browser with the most mature and polished interface was rated higher for usability, and semantic links were used by the users of all three browsers. Confirmation or contradiction of our original hypotheses with relation to SWBs is detailed along with observations of implementation issues.

SAS- Semantic Annotation Service for Geoscience resources on the web

NASA Astrophysics Data System (ADS)

Elag, M.; Kumar, P.; Marini, L.; Li, R.; Jiang, P.

2015-12-01

There is a growing need for increased integration across the data and model resources that are disseminated on the web to advance their reuse across different earth science applications. Meaningful reuse of resources requires semantic metadata to realize the semantic web vision for allowing pragmatic linkage and integration among resources. Semantic metadata associates standard metadata with resources to turn them into semantically-enabled resources on the web. However, the lack of a common standardized metadata framework as well as the uncoordinated use of metadata fields across different geo-information systems, has led to a situation in which standards and related Standard Names abound. To address this need, we have designed SAS to provide a bridge between the core ontologies required to annotate resources and information systems in order to enable queries and analysis over annotation from a single environment (web). SAS is one of the services that are provided by the Geosematnic framework, which is a decentralized semantic framework to support the integration between models and data and allow semantically heterogeneous to interact with minimum human intervention. Here we present the design of SAS and demonstrate its application for annotating data and models. First we describe how predicates and their attributes are extracted from standards and ingested in the knowledge-base of the Geosemantic framework. Then we illustrate the application of SAS in annotating data managed by SEAD and annotating simulation models that have web interface. SAS is a step in a broader approach to raise the quality of geoscience data and models that are published on the web and allow users to better search, access, and use of the existing resources based on standard vocabularies that are encoded and published using semantic technologies.

E-Government Goes Semantic Web: How Administrations Can Transform Their Information Processes

NASA Astrophysics Data System (ADS)

Klischewski, Ralf; Ukena, Stefan

E-government applications and services are built mainly on access to, retrieval of, integration of, and delivery of relevant information to citizens, businesses, and administrative users. In order to perform such information processing automatically through the Semantic Web,1 machine-readable2 enhancements of web resources are needed, based on the understanding of the content and context of the information in focus. While these enhancements are far from trivial to produce, administrations in their role of information and service providers so far find little guidance on how to migrate their web resources and enable a new quality of information processing; even research is still seeking best practices. Therefore, the underlying research question of this chapter is: what are the appropriate approaches which guide administrations in transforming their information processes toward the Semantic Web? In search for answers, this chapter analyzes the challenges and possible solutions from the perspective of administrations: (a) the reconstruction of the information processing in the e-government in terms of how semantic technologies must be employed to support information provision and consumption through the Semantic Web; (b) the required contribution to the transformation is compared to the capabilities and expectations of administrations; and (c) available experience with the steps of transformation are reviewed and discussed as to what extent they can be expected to successfully drive the e-government to the Semantic Web. This research builds on studying the case of Schleswig-Holstein, Germany, where semantic technologies have been used within the frame of the Access-eGov3 project in order to semantically enhance electronic service interfaces with the aim of providing a new way of accessing and combining e-government services.

Social Semantics for an Effective Enterprise

NASA Technical Reports Server (NTRS)

Berndt, Sarah; Doane, Mike

2012-01-01

An evolution of the Semantic Web, the Social Semantic Web (s2w), facilitates knowledge sharing with "useful information based on human contributions, which gets better as more people participate." The s2w reaches beyond the search box to move us from a collection of hyperlinked facts, to meaningful, real time context. When focused through the lens of Enterprise Search, the Social Semantic Web facilitates the fluid transition of meaningful business information from the source to the user. It is the confluence of human thought and computer processing structured with the iterative application of taxonomies, folksonomies, ontologies, and metadata schemas. The importance and nuances of human interaction are often deemphasized when focusing on automatic generation of semantic markup, which results in dissatisfied users and unrealized return on investment. Users consistently qualify the value of information sets through the act of selection, making them the de facto stakeholders of the Social Semantic Web. Employers are the ultimate beneficiaries of s2w utilization with a better informed, more decisive workforce; one not achieved with an IT miracle technology, but by improved human-computer interactions. Johnson Space Center Taxonomist Sarah Berndt and Mike Doane, principal owner of Term Management, LLC discuss the planning, development, and maintenance stages for components of a semantic system while emphasizing the necessity of a Social Semantic Web for the Enterprise. Identification of risks and variables associated with layering the successful implementation of a semantic system are also modeled.

Informatics in radiology: radiology gamuts ontology: differential diagnosis for the Semantic Web.

PubMed

Budovec, Joseph J; Lam, Cesar A; Kahn, Charles E

2014-01-01

The Semantic Web is an effort to add semantics, or "meaning," to empower automated searching and processing of Web-based information. The overarching goal of the Semantic Web is to enable users to more easily find, share, and combine information. Critical to this vision are knowledge models called ontologies, which define a set of concepts and formalize the relations between them. Ontologies have been developed to manage and exploit the large and rapidly growing volume of information in biomedical domains. In diagnostic radiology, lists of differential diagnoses of imaging observations, called gamuts, provide an important source of knowledge. The Radiology Gamuts Ontology (RGO) is a formal knowledge model of differential diagnoses in radiology that includes 1674 differential diagnoses, 19,017 terms, and 52,976 links between terms. Its knowledge is used to provide an interactive, freely available online reference of radiology gamuts ( www.gamuts.net ). A Web service allows its content to be discovered and consumed by other information systems. The RGO integrates radiologic knowledge with other biomedical ontologies as part of the Semantic Web. © RSNA, 2014.

Standard biological parts knowledgebase.

PubMed

Galdzicki, Michal; Rodriguez, Cesar; Chandran, Deepak; Sauro, Herbert M; Gennari, John H

2011-02-24

We have created the Knowledgebase of Standard Biological Parts (SBPkb) as a publically accessible Semantic Web resource for synthetic biology (sbolstandard.org). The SBPkb allows researchers to query and retrieve standard biological parts for research and use in synthetic biology. Its initial version includes all of the information about parts stored in the Registry of Standard Biological Parts (partsregistry.org). SBPkb transforms this information so that it is computable, using our semantic framework for synthetic biology parts. This framework, known as SBOL-semantic, was built as part of the Synthetic Biology Open Language (SBOL), a project of the Synthetic Biology Data Exchange Group. SBOL-semantic represents commonly used synthetic biology entities, and its purpose is to improve the distribution and exchange of descriptions of biological parts. In this paper, we describe the data, our methods for transformation to SBPkb, and finally, we demonstrate the value of our knowledgebase with a set of sample queries. We use RDF technology and SPARQL queries to retrieve candidate "promoter" parts that are known to be both negatively and positively regulated. This method provides new web based data access to perform searches for parts that are not currently possible.

The Semantic Web in Education

ERIC Educational Resources Information Center

Ohler, Jason

2008-01-01

The semantic web or Web 3.0 makes information more meaningful to people by making it more understandable to machines. In this article, the author examines the implications of Web 3.0 for education. The author considers three areas of impact: knowledge construction, personal learning network maintenance, and personal educational administration.…

Moby and Moby 2: creatures of the deep (web).

PubMed

Vandervalk, Ben P; McCarthy, E Luke; Wilkinson, Mark D

2009-03-01

Facile and meaningful integration of data from disparate resources is the 'holy grail' of bioinformatics. Some resources have begun to address this problem by providing their data using Semantic Web standards, specifically the Resource Description Framework (RDF) and the Web Ontology Language (OWL). Unfortunately, adoption of Semantic Web standards has been slow overall, and even in cases where the standards are being utilized, interconnectivity between resources is rare. In response, we have seen the emergence of centralized 'semantic warehouses' that collect public data from third parties, integrate it, translate it into OWL/RDF and provide it to the community as a unified and queryable resource. One limitation of the warehouse approach is that queries are confined to the resources that have been selected for inclusion. A related problem, perhaps of greater concern, is that the majority of bioinformatics data exists in the 'Deep Web'-that is, the data does not exist until an application or analytical tool is invoked, and therefore does not have a predictable Web address. The inability to utilize Uniform Resource Identifiers (URIs) to address this data is a barrier to its accessibility via URI-centric Semantic Web technologies. Here we examine 'The State of the Union' for the adoption of Semantic Web standards in the health care and life sciences domain by key bioinformatics resources, explore the nature and connectivity of several community-driven semantic warehousing projects, and report on our own progress with the CardioSHARE/Moby-2 project, which aims to make the resources of the Deep Web transparently accessible through SPARQL queries.

Not Fade Away? Commentary to Paper "Education and The Semantic Web" ("IJAIED" Vol.14, 2004)

ERIC Educational Resources Information Center

Devedzic, Vladan

2016-01-01

If you ask me "Will Semantic Web 'ever' happen, in general, and specifically in education?", the best answer I can give you is "I don't know," but I know that today we are still far away from the hopes that I had when I wrote my paper "Education and The Semantic Web" (Devedzic 2004) more than 10 years ago. Much of the…

Privacy Preservation in Context-Aware Systems

DTIC Science & Technology

2011-01-01

Policies and the Semantic Web The Semantic Web refers to both a vision and a set of technologies. The vision was first articulated by Tim Berners - Lee ... Berners - lee 2005) is a distributed framework for describing and reasoning over policies in the Semantic Web. It supports N3 rules ( Berners - Lee ...Connolly 2008), ( Berners - Lee et al. 2005) for representing intercon- nections between policies and resources and uses the CWM forward-chaining reasoning

Publication and Retrieval of Computational Chemical-Physical Data Via the Semantic Web. Final Technical Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ostlund, Neil

This research showed the feasibility of applying the concepts of the Semantic Web to Computation Chemistry. We have created the first web portal (www.chemsem.com) that allows data created in the calculations of quantum chemistry, and other such chemistry calculations to be placed on the web in a way that makes the data accessible to scientists in a semantic form never before possible. The semantic web nature of the portal allows data to be searched, found, and used as an advance over the usual approach of a relational database. The semantic data on our portal has the nature of a Giantmore » Global Graph (GGG) that can be easily merged with related data and searched globally via a SPARQL Protocol and RDF Query Language (SPARQL) that makes global searches for data easier than with traditional methods. Our Semantic Web Portal requires that the data be understood by a computer and hence defined by an ontology (vocabulary). This ontology is used by the computer in understanding the data. We have created such an ontology for computational chemistry (purl.org/gc) that encapsulates a broad knowledge of the field of computational chemistry. We refer to this ontology as the Gainesville Core. While it is perhaps the first ontology for computational chemistry and is used by our portal, it is only a start of what must be a long multi-partner effort to define computational chemistry. In conjunction with the above efforts we have defined a new potential file standard (Common Standard for eXchange – CSX for computational chemistry data). This CSX file is the precursor of data in the Resource Description Framework (RDF) form that the semantic web requires. Our portal translates CSX files (as well as other computational chemistry data files) into RDF files that are part of the graph database that the semantic web employs. We propose a CSX file as a convenient way to encapsulate computational chemistry data.« less

Autonomous Mission Operations for Sensor Webs

NASA Astrophysics Data System (ADS)

Underbrink, A.; Witt, K.; Stanley, J.; Mandl, D.

2008-12-01

We present interim results of a 2005 ROSES AIST project entitled, "Using Intelligent Agents to Form a Sensor Web for Autonomous Mission Operations", or SWAMO. The goal of the SWAMO project is to shift the control of spacecraft missions from a ground-based, centrally controlled architecture to a collaborative, distributed set of intelligent agents. The network of intelligent agents intends to reduce management requirements by utilizing model-based system prediction and autonomic model/agent collaboration. SWAMO agents are distributed throughout the Sensor Web environment, which may include multiple spacecraft, aircraft, ground systems, and ocean systems, as well as manned operations centers. The agents monitor and manage sensor platforms, Earth sensing systems, and Earth sensing models and processes. The SWAMO agents form a Sensor Web of agents via peer-to-peer coordination. Some of the intelligent agents are mobile and able to traverse between on-orbit and ground-based systems. Other agents in the network are responsible for encapsulating system models to perform prediction of future behavior of the modeled subsystems and components to which they are assigned. The software agents use semantic web technologies to enable improved information sharing among the operational entities of the Sensor Web. The semantics include ontological conceptualizations of the Sensor Web environment, plus conceptualizations of the SWAMO agents themselves. By conceptualizations of the agents, we mean knowledge of their state, operational capabilities, current operational capacities, Web Service search and discovery results, agent collaboration rules, etc. The need for ontological conceptualizations over the agents is to enable autonomous and autonomic operations of the Sensor Web. The SWAMO ontology enables automated decision making and responses to the dynamic Sensor Web environment and to end user science requests. The current ontology is compatible with Open Geospatial Consortium (OGC) Sensor Web Enablement (SWE) Sensor Model Language (SensorML) concepts and structures. The agents are currently deployed on the U.S. Naval Academy MidSTAR-1 satellite and are actively managing the power subsystem on-orbit without the need for human intervention.

Web service discovery among large service pools utilising semantic similarity and clustering

NASA Astrophysics Data System (ADS)

Chen, Fuzan; Li, Minqiang; Wu, Harris; Xie, Lingli

2017-03-01

With the rapid development of electronic business, Web services have attracted much attention in recent years. Enterprises can combine individual Web services to provide new value-added services. An emerging challenge is the timely discovery of close matches to service requests among large service pools. In this study, we first define a new semantic similarity measure combining functional similarity and process similarity. We then present a service discovery mechanism that utilises the new semantic similarity measure for service matching. All the published Web services are pre-grouped into functional clusters prior to the matching process. For a user's service request, the discovery mechanism first identifies matching services clusters and then identifies the best matching Web services within these matching clusters. Experimental results show that the proposed semantic discovery mechanism performs better than a conventional lexical similarity-based mechanism.

SCALEUS: Semantic Web Services Integration for Biomedical Applications.

PubMed

Sernadela, Pedro; González-Castro, Lorena; Oliveira, José Luís

2017-04-01

In recent years, we have witnessed an explosion of biological data resulting largely from the demands of life science research. The vast majority of these data are freely available via diverse bioinformatics platforms, including relational databases and conventional keyword search applications. This type of approach has achieved great results in the last few years, but proved to be unfeasible when information needs to be combined or shared among different and scattered sources. During recent years, many of these data distribution challenges have been solved with the adoption of semantic web. Despite the evident benefits of this technology, its adoption introduced new challenges related with the migration process, from existent systems to the semantic level. To facilitate this transition, we have developed Scaleus, a semantic web migration tool that can be deployed on top of traditional systems in order to bring knowledge, inference rules, and query federation to the existent data. Targeted at the biomedical domain, this web-based platform offers, in a single package, straightforward data integration and semantic web services that help developers and researchers in the creation process of new semantically enhanced information systems. SCALEUS is available as open source at http://bioinformatics-ua.github.io/scaleus/ .

Semantic-Web Technology: Applications at NASA

NASA Technical Reports Server (NTRS)

Ashish, Naveen

2004-01-01

We provide a description of work at the National Aeronautics and Space Administration (NASA) on building system based on semantic-web concepts and technologies. NASA has been one of the early adopters of semantic-web technologies for practical applications. Indeed there are several ongoing 0 endeavors on building semantics based systems for use in diverse NASA domains ranging from collaborative scientific activity to accident and mishap investigation to enterprise search to scientific information gathering and integration to aviation safety decision support We provide a brief overview of many applications and ongoing work with the goal of informing the external community of these NASA endeavors.

Workspaces in the Semantic Web

NASA Technical Reports Server (NTRS)

Wolfe, Shawn R.; Keller, RIchard M.

2005-01-01

Due to the recency and relatively limited adoption of Semantic Web technologies. practical issues related to technology scaling have received less attention than foundational issues. Nonetheless, these issues must be addressed if the Semantic Web is to realize its full potential. In particular, we concentrate on the lack of scoping methods that reduce the size of semantic information spaces so they are more efficient to work with and more relevant to an agent's needs. We provide some intuition to motivate the need for such reduced information spaces, called workspaces, give a formal definition, and suggest possible methods of deriving them.

Recommendation of standardized health learning contents using archetypes and semantic web technologies.

PubMed

Legaz-García, María del Carmen; Martínez-Costa, Catalina; Menárguez-Tortosa, Marcos; Fernández-Breis, Jesualdo Tomás

2012-01-01

Linking Electronic Healthcare Records (EHR) content to educational materials has been considered a key international recommendation to enable clinical engagement and to promote patient safety. This would suggest citizens to access reliable information available on the web and to guide them properly. In this paper, we describe an approach in that direction, based on the use of dual model EHR standards and standardized educational contents. The recommendation method will be based on the semantic coverage of the learning content repository for a particular archetype, which will be calculated by applying semantic web technologies like ontologies and semantic annotations.

Versioning System for Distributed Ontology Development

DTIC Science & Technology

2016-02-02

Semantic   Web   community. For example, the distributed and isolated development requirement may apply to non‐cyber  range communities of public ontology... semantic   web .” However, we observe that the  maintenance of an ontology and its reuse is not a high priority for the majority of the publicly available... Semantic )  Web . AAAI Spring Symposium: Symbiotic Relationships between  Semantic   Web  and  Knowledge Engineering. 2008.  [LHK09] Matthias Loskyll

Using Web Ontology Language to Integrate Heterogeneous Databases in the Neurosciences

PubMed Central

Lam, Hugo Y.K.; Marenco, Luis; Shepherd, Gordon M.; Miller, Perry L.; Cheung, Kei-Hoi

2006-01-01

Integrative neuroscience involves the integration and analysis of diverse types of neuroscience data involving many different experimental techniques. This data will increasingly be distributed across many heterogeneous databases that are web-accessible. Currently, these databases do not expose their schemas (database structures) and their contents to web applications/agents in a standardized, machine-friendly way. This limits database interoperation. To address this problem, we describe a pilot project that illustrates how neuroscience databases can be expressed using the Web Ontology Language, which is a semantically-rich ontological language, as a common data representation language to facilitate complex cross-database queries. In this pilot project, an existing tool called “D2RQ” was used to translate two neuroscience databases (NeuronDB and CoCoDat) into OWL, and the resulting OWL ontologies were then merged. An OWL-based reasoner (Racer) was then used to provide a sophisticated query language (nRQL) to perform integrated queries across the two databases based on the merged ontology. This pilot project is one step toward exploring the use of semantic web technologies in the neurosciences. PMID:17238384

Ontology Alignment Architecture for Semantic Sensor Web Integration

PubMed Central

Fernandez, Susel; Marsa-Maestre, Ivan; Velasco, Juan R.; Alarcos, Bernardo

2013-01-01

Sensor networks are a concept that has become very popular in data acquisition and processing for multiple applications in different fields such as industrial, medicine, home automation, environmental detection, etc. Today, with the proliferation of small communication devices with sensors that collect environmental data, semantic Web technologies are becoming closely related with sensor networks. The linking of elements from Semantic Web technologies with sensor networks has been called Semantic Sensor Web and has among its main features the use of ontologies. One of the key challenges of using ontologies in sensor networks is to provide mechanisms to integrate and exchange knowledge from heterogeneous sources (that is, dealing with semantic heterogeneity). Ontology alignment is the process of bringing ontologies into mutual agreement by the automatic discovery of mappings between related concepts. This paper presents a system for ontology alignment in the Semantic Sensor Web which uses fuzzy logic techniques to combine similarity measures between entities of different ontologies. The proposed approach focuses on two key elements: the terminological similarity, which takes into account the linguistic and semantic information of the context of the entity's names, and the structural similarity, based on both the internal and relational structure of the concepts. This work has been validated using sensor network ontologies and the Ontology Alignment Evaluation Initiative (OAEI) tests. The results show that the proposed techniques outperform previous approaches in terms of precision and recall. PMID:24051523

Ontology alignment architecture for semantic sensor Web integration.

PubMed

Fernandez, Susel; Marsa-Maestre, Ivan; Velasco, Juan R; Alarcos, Bernardo

2013-09-18

Sensor networks are a concept that has become very popular in data acquisition and processing for multiple applications in different fields such as industrial, medicine, home automation, environmental detection, etc. Today, with the proliferation of small communication devices with sensors that collect environmental data, semantic Web technologies are becoming closely related with sensor networks. The linking of elements from Semantic Web technologies with sensor networks has been called Semantic Sensor Web and has among its main features the use of ontologies. One of the key challenges of using ontologies in sensor networks is to provide mechanisms to integrate and exchange knowledge from heterogeneous sources (that is, dealing with semantic heterogeneity). Ontology alignment is the process of bringing ontologies into mutual agreement by the automatic discovery of mappings between related concepts. This paper presents a system for ontology alignment in the Semantic Sensor Web which uses fuzzy logic techniques to combine similarity measures between entities of different ontologies. The proposed approach focuses on two key elements: the terminological similarity, which takes into account the linguistic and semantic information of the context of the entity's names, and the structural similarity, based on both the internal and relational structure of the concepts. This work has been validated using sensor network ontologies and the Ontology Alignment Evaluation Initiative (OAEI) tests. The results show that the proposed techniques outperform previous approaches in terms of precision and recall.

SADI, SHARE, and the in silico scientific method

PubMed Central

2010-01-01

Background The emergence and uptake of Semantic Web technologies by the Life Sciences provides exciting opportunities for exploring novel ways to conduct in silico science. Web Service Workflows are already becoming first-class objects in “the new way”, and serve as explicit, shareable, referenceable representations of how an experiment was done. In turn, Semantic Web Service projects aim to facilitate workflow construction by biological domain-experts such that workflows can be edited, re-purposed, and re-published by non-informaticians. However the aspects of the scientific method relating to explicit discourse, disagreement, and hypothesis generation have remained relatively impervious to new technologies. Results Here we present SADI and SHARE - a novel Semantic Web Service framework, and a reference implementation of its client libraries. Together, SADI and SHARE allow the semi- or fully-automatic discovery and pipelining of Semantic Web Services in response to ad hoc user queries. Conclusions The semantic behaviours exhibited by SADI and SHARE extend the functionalities provided by Description Logic Reasoners such that novel assertions can be automatically added to a data-set without logical reasoning, but rather by analytical or annotative services. This behaviour might be applied to achieve the “semantification” of those aspects of the in silico scientific method that are not yet supported by Semantic Web technologies. We support this suggestion using an example in the clinical research space. PMID:21210986

Towards Linked Open Services and Processes

NASA Astrophysics Data System (ADS)

Krummenacher, Reto; Norton, Barry; Marte, Adrian

The combination of semantic technology and Web services in form of 'Semantic Web Services' has until now been oriented towards extension of the WS-* stack with ontology-based descriptions. The same time, there is a strong movement away from this stack - for which the 'Web' part is little more than branding - towards RESTful services. The Linked Open Data initiative is a keen adopter of this approach and exposes many datasets via SPARQL endpoints and RESTful services. Our developing approach of 'Linked Open Services', whose current state is described in this paper, accommodates such Linked Data endpoints and general RESTful services alongside WS-* stack-based services with descriptions based on RDF and SPARQL. This capitalises on the Linked Data Cloud and makes service description and comprehension more easy and direct to the growing Linked Data community. Along the way, we show how the existing link between service messaging and the semantic viewpoint, commonly called 'lifting and lowering', is usually unduly restricted to ontology-based classification and misses how the effect of a service contributes to the knowledge of its consumer. Our SPARQL-based approach helps also in the composition of services as knowledge-centric processes, and encourages the development and exposure of services that communicate RDF.

The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies.

PubMed

Katayama, Toshiaki; Wilkinson, Mark D; Micklem, Gos; Kawashima, Shuichi; Yamaguchi, Atsuko; Nakao, Mitsuteru; Yamamoto, Yasunori; Okamoto, Shinobu; Oouchida, Kenta; Chun, Hong-Woo; Aerts, Jan; Afzal, Hammad; Antezana, Erick; Arakawa, Kazuharu; Aranda, Bruno; Belleau, Francois; Bolleman, Jerven; Bonnal, Raoul Jp; Chapman, Brad; Cock, Peter Ja; Eriksson, Tore; Gordon, Paul Mk; Goto, Naohisa; Hayashi, Kazuhiro; Horn, Heiko; Ishiwata, Ryosuke; Kaminuma, Eli; Kasprzyk, Arek; Kawaji, Hideya; Kido, Nobuhiro; Kim, Young Joo; Kinjo, Akira R; Konishi, Fumikazu; Kwon, Kyung-Hoon; Labarga, Alberto; Lamprecht, Anna-Lena; Lin, Yu; Lindenbaum, Pierre; McCarthy, Luke; Morita, Hideyuki; Murakami, Katsuhiko; Nagao, Koji; Nishida, Kozo; Nishimura, Kunihiro; Nishizawa, Tatsuya; Ogishima, Soichi; Ono, Keiichiro; Oshita, Kazuki; Park, Keun-Joon; Prins, Pjotr; Saito, Taro L; Samwald, Matthias; Satagopam, Venkata P; Shigemoto, Yasumasa; Smith, Richard; Splendiani, Andrea; Sugawara, Hideaki; Taylor, James; Vos, Rutger A; Withers, David; Yamasaki, Chisato; Zmasek, Christian M; Kawamoto, Shoko; Okubo, Kosaku; Asai, Kiyoshi; Takagi, Toshihisa

2013-02-11

BioHackathon 2010 was the third in a series of meetings hosted by the Database Center for Life Sciences (DBCLS) in Tokyo, Japan. The overall goal of the BioHackathon series is to improve the quality and accessibility of life science research data on the Web by bringing together representatives from public databases, analytical tool providers, and cyber-infrastructure researchers to jointly tackle important challenges in the area of in silico biological research. The theme of BioHackathon 2010 was the 'Semantic Web', and all attendees gathered with the shared goal of producing Semantic Web data from their respective resources, and/or consuming or interacting those data using their tools and interfaces. We discussed on topics including guidelines for designing semantic data and interoperability of resources. We consequently developed tools and clients for analysis and visualization. We provide a meeting report from BioHackathon 2010, in which we describe the discussions, decisions, and breakthroughs made as we moved towards compliance with Semantic Web technologies - from source provider, through middleware, to the end-consumer.

The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies

PubMed Central

2013-01-01

Background BioHackathon 2010 was the third in a series of meetings hosted by the Database Center for Life Sciences (DBCLS) in Tokyo, Japan. The overall goal of the BioHackathon series is to improve the quality and accessibility of life science research data on the Web by bringing together representatives from public databases, analytical tool providers, and cyber-infrastructure researchers to jointly tackle important challenges in the area of in silico biological research. Results The theme of BioHackathon 2010 was the 'Semantic Web', and all attendees gathered with the shared goal of producing Semantic Web data from their respective resources, and/or consuming or interacting those data using their tools and interfaces. We discussed on topics including guidelines for designing semantic data and interoperability of resources. We consequently developed tools and clients for analysis and visualization. Conclusion We provide a meeting report from BioHackathon 2010, in which we describe the discussions, decisions, and breakthroughs made as we moved towards compliance with Semantic Web technologies - from source provider, through middleware, to the end-consumer. PMID:23398680

Process model-based atomic service discovery and composition of composite semantic web services using web ontology language for services (OWL-S)

NASA Astrophysics Data System (ADS)

Paulraj, D.; Swamynathan, S.; Madhaiyan, M.

2012-11-01

Web Service composition has become indispensable as a single web service cannot satisfy complex functional requirements. Composition of services has received much interest to support business-to-business (B2B) or enterprise application integration. An important component of the service composition is the discovery of relevant services. In Semantic Web Services (SWS), service discovery is generally achieved by using service profile of Ontology Web Languages for Services (OWL-S). The profile of the service is a derived and concise description but not a functional part of the service. The information contained in the service profile is sufficient for atomic service discovery, but it is not sufficient for the discovery of composite semantic web services (CSWS). The purpose of this article is two-fold: first to prove that the process model is a better choice than the service profile for service discovery. Second, to facilitate the composition of inter-organisational CSWS by proposing a new composition method which uses process ontology. The proposed service composition approach uses an algorithm which performs a fine grained match at the level of atomic process rather than at the level of the entire service in a composite semantic web service. Many works carried out in this area have proposed solutions only for the composition of atomic services and this article proposes a solution for the composition of composite semantic web services.

A Query Integrator and Manager for the Query Web

PubMed Central

Brinkley, James F.; Detwiler, Landon T.

2012-01-01

We introduce two concepts: the Query Web as a layer of interconnected queries over the document web and the semantic web, and a Query Web Integrator and Manager (QI) that enables the Query Web to evolve. QI permits users to write, save and reuse queries over any web accessible source, including other queries saved in other installations of QI. The saved queries may be in any language (e.g. SPARQL, XQuery); the only condition for interconnection is that the queries return their results in some form of XML. This condition allows queries to chain off each other, and to be written in whatever language is appropriate for the task. We illustrate the potential use of QI for several biomedical use cases, including ontology view generation using a combination of graph-based and logical approaches, value set generation for clinical data management, image annotation using terminology obtained from an ontology web service, ontology-driven brain imaging data integration, small-scale clinical data integration, and wider-scale clinical data integration. Such use cases illustrate the current range of applications of QI and lead us to speculate about the potential evolution from smaller groups of interconnected queries into a larger query network that layers over the document and semantic web. The resulting Query Web could greatly aid researchers and others who now have to manually navigate through multiple information sources in order to answer specific questions. PMID:22531831

Semantator: semantic annotator for converting biomedical text to linked data.

PubMed

Tao, Cui; Song, Dezhao; Sharma, Deepak; Chute, Christopher G

2013-10-01

More than 80% of biomedical data is embedded in plain text. The unstructured nature of these text-based documents makes it challenging to easily browse and query the data of interest in them. One approach to facilitate browsing and querying biomedical text is to convert the plain text to a linked web of data, i.e., converting data originally in free text to structured formats with defined meta-level semantics. In this paper, we introduce Semantator (Semantic Annotator), a semantic-web-based environment for annotating data of interest in biomedical documents, browsing and querying the annotated data, and interactively refining annotation results if needed. Through Semantator, information of interest can be either annotated manually or semi-automatically using plug-in information extraction tools. The annotated results will be stored in RDF and can be queried using the SPARQL query language. In addition, semantic reasoners can be directly applied to the annotated data for consistency checking and knowledge inference. Semantator has been released online and was used by the biomedical ontology community who provided positive feedbacks. Our evaluation results indicated that (1) Semantator can perform the annotation functionalities as designed; (2) Semantator can be adopted in real applications in clinical and transactional research; and (3) the annotated results using Semantator can be easily used in Semantic-web-based reasoning tools for further inference. Copyright © 2013 Elsevier Inc. All rights reserved.

Sealife: a semantic grid browser for the life sciences applied to the study of infectious diseases.

PubMed

Schroeder, Michael; Burger, Albert; Kostkova, Patty; Stevens, Robert; Habermann, Bianca; Dieng-Kuntz, Rose

2006-01-01

The objective of Sealife is the conception and realisation of a semantic Grid browser for the life sciences, which will link the existing Web to the currently emerging eScience infrastructure. The SeaLife Browser will allow users to automatically link a host of Web servers and Web/Grid services to the Web content he/she is visiting. This will be accomplished using eScience's growing number of Web/Grid Services and its XML-based standards and ontologies. The browser will identify terms in the pages being browsed through the background knowledge held in ontologies. Through the use of Semantic Hyperlinks, which link identified ontology terms to servers and services, the SeaLife Browser will offer a new dimension of context-based information integration. In this paper, we give an overview over the different components of the browser and their interplay. This SeaLife Browser will be demonstrated within three application scenarios in evidence-based medicine, literature & patent mining, and molecular biology, all relating to the study of infectious diseases. The three applications vertically integrate the molecule/cell, the tissue/organ and the patient/population level by covering the analysis of high-throughput screening data for endocytosis (the molecular entry pathway into the cell), the expression of proteins in the spatial context of tissue and organs, and a high-level library on infectious diseases designed for clinicians and their patients. For more information see http://www.biote.ctu-dresden.de/sealife.

Progress toward a Semantic eScience Framework; building on advanced cyberinfrastructure

NASA Astrophysics Data System (ADS)

McGuinness, D. L.; Fox, P. A.; West, P.; Rozell, E.; Zednik, S.; Chang, C.

2010-12-01

The configurable and extensible semantic eScience framework (SESF) has begun development and implementation of several semantic application components. Extensions and improvements to several ontologies have been made based on distinct interdisciplinary use cases ranging from solar physics, to biologicl and chemical oceanography. Importantly, these semantic representations mediate access to a diverse set of existing and emerging cyberinfrastructure. Among the advances are the population of triple stores with web accessible query services. A triple store is akin to a relational data store where the basic stored unit is a subject-predicate-object tuple. Access via a query is provided by the W3 Recommendation language specification SPARQL. Upon this middle tier of semantic cyberinfrastructure, we have developed several forms of semantic faceted search, including provenance-awareness. We report on the rapid advances in semantic technologies and tools and how we are sustaining the software path for the required technical advances as well as the ontology improvements and increased functionality of the semantic applications including how they are integrated into web-based portals (e.g. Drupal) and web services. Lastly, we indicate future work direction and opportunities for collaboration.

Semantic similarity measure in biomedical domain leverage web search engine.

PubMed

Chen, Chi-Huang; Hsieh, Sheau-Ling; Weng, Yung-Ching; Chang, Wen-Yung; Lai, Feipei

2010-01-01

Semantic similarity measure plays an essential role in Information Retrieval and Natural Language Processing. In this paper we propose a page-count-based semantic similarity measure and apply it in biomedical domains. Previous researches in semantic web related applications have deployed various semantic similarity measures. Despite the usefulness of the measurements in those applications, measuring semantic similarity between two terms remains a challenge task. The proposed method exploits page counts returned by the Web Search Engine. We define various similarity scores for two given terms P and Q, using the page counts for querying P, Q and P AND Q. Moreover, we propose a novel approach to compute semantic similarity using lexico-syntactic patterns with page counts. These different similarity scores are integrated adapting support vector machines, to leverage the robustness of semantic similarity measures. Experimental results on two datasets achieve correlation coefficients of 0.798 on the dataset provided by A. Hliaoutakis, 0.705 on the dataset provide by T. Pedersen with physician scores and 0.496 on the dataset provided by T. Pedersen et al. with expert scores.

Semantic representation of CDC-PHIN vocabulary using Simple Knowledge Organization System.

PubMed

Zhu, Min; Mirhaji, Parsa

2008-11-06

PHIN Vocabulary Access and Distribution System (VADS) promotes the use of standards based vocabulary within CDC information systems. However, the current PHIN vocabulary representation hinders its wide adoption. Simple Knowledge Organization System (SKOS) is a W3C draft specification to support the formal representation of Knowledge Organization Systems (KOS) within the framework of the Semantic Web. We present a method of adopting SKOS to represent PHIN vocabulary in order to enable automated information sharing and integration.

Automatic Semantic Generation and Arabic Translation of Mathematical Expressions on the Web

ERIC Educational Resources Information Center

Doush, Iyad Abu; Al-Bdarneh, Sondos

2013-01-01

Automatic processing of mathematical information on the web imposes some difficulties. This paper presents a novel technique for automatic generation of mathematical equations semantic and Arabic translation on the web. The proposed system facilitates unambiguous representation of mathematical equations by correlating equations to their known…

UltiMatch-NL: A Web Service Matchmaker Based on Multiple Semantic Filters

PubMed Central

Mohebbi, Keyvan; Ibrahim, Suhaimi; Zamani, Mazdak; Khezrian, Mojtaba

2014-01-01

In this paper, a Semantic Web service matchmaker called UltiMatch-NL is presented. UltiMatch-NL applies two filters namely Signature-based and Description-based on different abstraction levels of a service profile to achieve more accurate results. More specifically, the proposed filters rely on semantic knowledge to extract the similarity between a given pair of service descriptions. Thus it is a further step towards fully automated Web service discovery via making this process more semantic-aware. In addition, a new technique is proposed to weight and combine the results of different filters of UltiMatch-NL, automatically. Moreover, an innovative approach is introduced to predict the relevance of requests and Web services and eliminate the need for setting a threshold value of similarity. In order to evaluate UltiMatch-NL, the repository of OWLS-TC is used. The performance evaluation based on standard measures from the information retrieval field shows that semantic matching of OWL-S services can be significantly improved by incorporating designed matching filters. PMID:25157872

Recipes for Semantic Web Dog Food — The ESWC and ISWC Metadata Projects

NASA Astrophysics Data System (ADS)

Möller, Knud; Heath, Tom; Handschuh, Siegfried; Domingue, John

Semantic Web conferences such as ESWC and ISWC offer prime opportunities to test and showcase semantic technologies. Conference metadata about people, papers and talks is diverse in nature and neither too small to be uninteresting or too big to be unmanageable. Many metadata-related challenges that may arise in the Semantic Web at large are also present here. Metadata must be generated from sources which are often unstructured and hard to process, and may originate from many different players, therefore suitable workflows must be established. Moreover, the generated metadata must use appropriate formats and vocabularies, and be served in a way that is consistent with the principles of linked data. This paper reports on the metadata efforts from ESWC and ISWC, identifies specific issues and barriers encountered during the projects, and discusses how these were approached. Recommendations are made as to how these may be addressed in the future, and we discuss how these solutions may generalize to metadata production for the Semantic Web at large.

ADEpedia: a scalable and standardized knowledge base of Adverse Drug Events using semantic web technology.

PubMed

Jiang, Guoqian; Solbrig, Harold R; Chute, Christopher G

2011-01-01

A source of semantically coded Adverse Drug Event (ADE) data can be useful for identifying common phenotypes related to ADEs. We proposed a comprehensive framework for building a standardized ADE knowledge base (called ADEpedia) through combining ontology-based approach with semantic web technology. The framework comprises four primary modules: 1) an XML2RDF transformation module; 2) a data normalization module based on NCBO Open Biomedical Annotator; 3) a RDF store based persistence module; and 4) a front-end module based on a Semantic Wiki for the review and curation. A prototype is successfully implemented to demonstrate the capability of the system to integrate multiple drug data and ontology resources and open web services for the ADE data standardization. A preliminary evaluation is performed to demonstrate the usefulness of the system, including the performance of the NCBO annotator. In conclusion, the semantic web technology provides a highly scalable framework for ADE data source integration and standard query service.

UltiMatch-NL: a Web service matchmaker based on multiple semantic filters.

PubMed

Mohebbi, Keyvan; Ibrahim, Suhaimi; Zamani, Mazdak; Khezrian, Mojtaba

2014-01-01

In this paper, a Semantic Web service matchmaker called UltiMatch-NL is presented. UltiMatch-NL applies two filters namely Signature-based and Description-based on different abstraction levels of a service profile to achieve more accurate results. More specifically, the proposed filters rely on semantic knowledge to extract the similarity between a given pair of service descriptions. Thus it is a further step towards fully automated Web service discovery via making this process more semantic-aware. In addition, a new technique is proposed to weight and combine the results of different filters of UltiMatch-NL, automatically. Moreover, an innovative approach is introduced to predict the relevance of requests and Web services and eliminate the need for setting a threshold value of similarity. In order to evaluate UltiMatch-NL, the repository of OWLS-TC is used. The performance evaluation based on standard measures from the information retrieval field shows that semantic matching of OWL-S services can be significantly improved by incorporating designed matching filters.

Standard Biological Parts Knowledgebase

PubMed Central

Galdzicki, Michal; Rodriguez, Cesar; Chandran, Deepak; Sauro, Herbert M.; Gennari, John H.

2011-01-01

We have created the Knowledgebase of Standard Biological Parts (SBPkb) as a publically accessible Semantic Web resource for synthetic biology (sbolstandard.org). The SBPkb allows researchers to query and retrieve standard biological parts for research and use in synthetic biology. Its initial version includes all of the information about parts stored in the Registry of Standard Biological Parts (partsregistry.org). SBPkb transforms this information so that it is computable, using our semantic framework for synthetic biology parts. This framework, known as SBOL-semantic, was built as part of the Synthetic Biology Open Language (SBOL), a project of the Synthetic Biology Data Exchange Group. SBOL-semantic represents commonly used synthetic biology entities, and its purpose is to improve the distribution and exchange of descriptions of biological parts. In this paper, we describe the data, our methods for transformation to SBPkb, and finally, we demonstrate the value of our knowledgebase with a set of sample queries. We use RDF technology and SPARQL queries to retrieve candidate “promoter” parts that are known to be both negatively and positively regulated. This method provides new web based data access to perform searches for parts that are not currently possible. PMID:21390321

SemanticSCo: A platform to support the semantic composition of services for gene expression analysis.

PubMed

Guardia, Gabriela D A; Ferreira Pires, Luís; da Silva, Eduardo G; de Farias, Cléver R G

2017-02-01

Gene expression studies often require the combined use of a number of analysis tools. However, manual integration of analysis tools can be cumbersome and error prone. To support a higher level of automation in the integration process, efforts have been made in the biomedical domain towards the development of semantic web services and supporting composition environments. Yet, most environments consider only the execution of simple service behaviours and requires users to focus on technical details of the composition process. We propose a novel approach to the semantic composition of gene expression analysis services that addresses the shortcomings of the existing solutions. Our approach includes an architecture designed to support the service composition process for gene expression analysis, and a flexible strategy for the (semi) automatic composition of semantic web services. Finally, we implement a supporting platform called SemanticSCo to realize the proposed composition approach and demonstrate its functionality by successfully reproducing a microarray study documented in the literature. The SemanticSCo platform provides support for the composition of RESTful web services semantically annotated using SAWSDL. Our platform also supports the definition of constraints/conditions regarding the order in which service operations should be invoked, thus enabling the definition of complex service behaviours. Our proposed solution for semantic web service composition takes into account the requirements of different stakeholders and addresses all phases of the service composition process. It also provides support for the definition of analysis workflows at a high-level of abstraction, thus enabling users to focus on biological research issues rather than on the technical details of the composition process. The SemanticSCo source code is available at https://github.com/usplssb/SemanticSCo. Copyright © 2017 Elsevier Inc. All rights reserved.

Improving life sciences information retrieval using semantic web technology.

PubMed

Quan, Dennis

2007-05-01

The ability to retrieve relevant information is at the heart of every aspect of research and development in the life sciences industry. Information is often distributed across multiple systems and recorded in a way that makes it difficult to piece together the complete picture. Differences in data formats, naming schemes and network protocols amongst information sources, both public and private, must be overcome, and user interfaces not only need to be able to tap into these diverse information sources but must also assist users in filtering out extraneous information and highlighting the key relationships hidden within an aggregated set of information. The Semantic Web community has made great strides in proposing solutions to these problems, and many efforts are underway to apply Semantic Web techniques to the problem of information retrieval in the life sciences space. This article gives an overview of the principles underlying a Semantic Web-enabled information retrieval system: creating a unified abstraction for knowledge using the RDF semantic network model; designing semantic lenses that extract contextually relevant subsets of information; and assembling semantic lenses into powerful information displays. Furthermore, concrete examples of how these principles can be applied to life science problems including a scenario involving a drug discovery dashboard prototype called BioDash are provided.

Accelerating Cancer Systems Biology Research through Semantic Web Technology

PubMed Central

Wang, Zhihui; Sagotsky, Jonathan; Taylor, Thomas; Shironoshita, Patrick; Deisboeck, Thomas S.

2012-01-01

Cancer systems biology is an interdisciplinary, rapidly expanding research field in which collaborations are a critical means to advance the field. Yet the prevalent database technologies often isolate data rather than making it easily accessible. The Semantic Web has the potential to help facilitate web-based collaborative cancer research by presenting data in a manner that is self-descriptive, human and machine readable, and easily sharable. We have created a semantically linked online Digital Model Repository (DMR) for storing, managing, executing, annotating, and sharing computational cancer models. Within the DMR, distributed, multidisciplinary, and inter-organizational teams can collaborate on projects, without forfeiting intellectual property. This is achieved by the introduction of a new stakeholder to the collaboration workflow, the institutional licensing officer, part of the Technology Transfer Office. Furthermore, the DMR has achieved silver level compatibility with the National Cancer Institute’s caBIG®, so users can not only interact with the DMR through a web browser but also through a semantically annotated and secure web service. We also discuss the technology behind the DMR leveraging the Semantic Web, ontologies, and grid computing to provide secure inter-institutional collaboration on cancer modeling projects, online grid-based execution of shared models, and the collaboration workflow protecting researchers’ intellectual property. PMID:23188758

Accelerating cancer systems biology research through Semantic Web technology.

PubMed

Wang, Zhihui; Sagotsky, Jonathan; Taylor, Thomas; Shironoshita, Patrick; Deisboeck, Thomas S

2013-01-01

Cancer systems biology is an interdisciplinary, rapidly expanding research field in which collaborations are a critical means to advance the field. Yet the prevalent database technologies often isolate data rather than making it easily accessible. The Semantic Web has the potential to help facilitate web-based collaborative cancer research by presenting data in a manner that is self-descriptive, human and machine readable, and easily sharable. We have created a semantically linked online Digital Model Repository (DMR) for storing, managing, executing, annotating, and sharing computational cancer models. Within the DMR, distributed, multidisciplinary, and inter-organizational teams can collaborate on projects, without forfeiting intellectual property. This is achieved by the introduction of a new stakeholder to the collaboration workflow, the institutional licensing officer, part of the Technology Transfer Office. Furthermore, the DMR has achieved silver level compatibility with the National Cancer Institute's caBIG, so users can interact with the DMR not only through a web browser but also through a semantically annotated and secure web service. We also discuss the technology behind the DMR leveraging the Semantic Web, ontologies, and grid computing to provide secure inter-institutional collaboration on cancer modeling projects, online grid-based execution of shared models, and the collaboration workflow protecting researchers' intellectual property. Copyright © 2012 Wiley Periodicals, Inc.

Auditing the NCI Thesaurus with Semantic Web Technologies

PubMed Central

Mougin, Fleur; Bodenreider, Olivier

2008-01-01

Auditing biomedical terminologies often results in the identification of inconsistencies and thus helps to improve their quality. In this paper, we present a method based on Semantic Web technologies for auditing biomedical terminologies and apply it to the NCI thesaurus. We stored the NCI thesaurus concepts and their properties in an RDF triple store. By querying this store, we assessed the consistency of both hierarchical and associative relations from the NCI thesaurus among themselves and with corresponding relations in the UMLS Semantic Network. We show that the consistency is better for associative relations than for hierarchical relations. Causes for inconsistency and benefits from using Semantic Web technologies for auditing purposes are discussed. PMID:18999265

Auditing the NCI thesaurus with semantic web technologies.

PubMed

Mougin, Fleur; Bodenreider, Olivier

2008-11-06

Auditing biomedical terminologies often results in the identification of inconsistencies and thus helps to improve their quality. In this paper, we present a method based on Semantic Web technologies for auditing biomedical terminologies and apply it to the NCI thesaurus. We stored the NCI thesaurus concepts and their properties in an RDF triple store. By querying this store, we assessed the consistency of both hierarchical and associative relations from the NCI thesaurus among themselves and with corresponding relations in the UMLS Semantic Network. We show that the consistency is better for associative relations than for hierarchical relations. Causes for inconsistency and benefits from using Semantic Web technologies for auditing purposes are discussed.

A semantic web ontology for small molecules and their biological targets.

PubMed

Choi, Jooyoung; Davis, Melissa J; Newman, Andrew F; Ragan, Mark A

2010-05-24

A wide range of data on sequences, structures, pathways, and networks of genes and gene products is available for hypothesis testing and discovery in biological and biomedical research. However, data describing the physical, chemical, and biological properties of small molecules have not been well-integrated with these resources. Semantically rich representations of chemical data, combined with Semantic Web technologies, have the potential to enable the integration of small molecule and biomolecular data resources, expanding the scope and power of biomedical and pharmacological research. We employed the Semantic Web technologies Resource Description Framework (RDF) and Web Ontology Language (OWL) to generate a Small Molecule Ontology (SMO) that represents concepts and provides unique identifiers for biologically relevant properties of small molecules and their interactions with biomolecules, such as proteins. We instanced SMO using data from three public data sources, i.e., DrugBank, PubChem and UniProt, and converted to RDF triples. Evaluation of SMO by use of predetermined competency questions implemented as SPARQL queries demonstrated that data from chemical and biomolecular data sources were effectively represented and that useful knowledge can be extracted. These results illustrate the potential of Semantic Web technologies in chemical, biological, and pharmacological research and in drug discovery.

A Ubiquitous Sensor Network Platform for Integrating Smart Devices into the Semantic Sensor Web

PubMed Central

de Vera, David Díaz Pardo; Izquierdo, Álvaro Sigüenza; Vercher, Jesús Bernat; Gómez, Luis Alfonso Hernández

2014-01-01

Ongoing Sensor Web developments make a growing amount of heterogeneous sensor data available to smart devices. This is generating an increasing demand for homogeneous mechanisms to access, publish and share real-world information. This paper discusses, first, an architectural solution based on Next Generation Networks: a pilot Telco Ubiquitous Sensor Network (USN) Platform that embeds several OGC® Sensor Web services. This platform has already been deployed in large scale projects. Second, the USN-Platform is extended to explore a first approach to Semantic Sensor Web principles and technologies, so that smart devices can access Sensor Web data, allowing them also to share richer (semantically interpreted) information. An experimental scenario is presented: a smart car that consumes and produces real-world information which is integrated into the Semantic Sensor Web through a Telco USN-Platform. Performance tests revealed that observation publishing times with our experimental system were well within limits compatible with the adequate operation of smart safety assistance systems in vehicles. On the other hand, response times for complex queries on large repositories may be inappropriate for rapid reaction needs. PMID:24945678

A ubiquitous sensor network platform for integrating smart devices into the semantic sensor web.

PubMed

de Vera, David Díaz Pardo; Izquierdo, Alvaro Sigüenza; Vercher, Jesús Bernat; Hernández Gómez, Luis Alfonso

2014-06-18

Ongoing Sensor Web developments make a growing amount of heterogeneous sensor data available to smart devices. This is generating an increasing demand for homogeneous mechanisms to access, publish and share real-world information. This paper discusses, first, an architectural solution based on Next Generation Networks: a pilot Telco Ubiquitous Sensor Network (USN) Platform that embeds several OGC® Sensor Web services. This platform has already been deployed in large scale projects. Second, the USN-Platform is extended to explore a first approach to Semantic Sensor Web principles and technologies, so that smart devices can access Sensor Web data, allowing them also to share richer (semantically interpreted) information. An experimental scenario is presented: a smart car that consumes and produces real-world information which is integrated into the Semantic Sensor Web through a Telco USN-Platform. Performance tests revealed that observation publishing times with our experimental system were well within limits compatible with the adequate operation of smart safety assistance systems in vehicles. On the other hand, response times for complex queries on large repositories may be inappropriate for rapid reaction needs.

Semantic Networks and Social Networks

ERIC Educational Resources Information Center

Downes, Stephen

2005-01-01

Purpose: To illustrate the need for social network metadata within semantic metadata. Design/methodology/approach: Surveys properties of social networks and the semantic web, suggests that social network analysis applies to semantic content, argues that semantic content is more searchable if social network metadata is merged with semantic web…

Usage and applications of Semantic Web techniques and technologies to support chemistry research

PubMed Central

2014-01-01

Background The drug discovery process is now highly dependent on the management, curation and integration of large amounts of potentially useful data. Semantics are necessary in order to interpret the information and derive knowledge. Advances in recent years have mitigated concerns that the lack of robust, usable tools has inhibited the adoption of methodologies based on semantics. Results This paper presents three examples of how Semantic Web techniques and technologies can be used in order to support chemistry research: a controlled vocabulary for quantities, units and symbols in physical chemistry; a controlled vocabulary for the classification and labelling of chemical substances and mixtures; and, a database of chemical identifiers. This paper also presents a Web-based service that uses the datasets in order to assist with the completion of risk assessment forms, along with a discussion of the legal implications and value-proposition for the use of such a service. Conclusions We have introduced the Semantic Web concepts, technologies, and methodologies that can be used to support chemistry research, and have demonstrated the application of those techniques in three areas very relevant to modern chemistry research, generating three new datasets that we offer as exemplars of an extensible portfolio of advanced data integration facilities. We have thereby established the importance of Semantic Web techniques and technologies for meeting Wild’s fourth “grand challenge”. PMID:24855494

Usage and applications of Semantic Web techniques and technologies to support chemistry research.

PubMed

Borkum, Mark I; Frey, Jeremy G

2014-01-01

The drug discovery process is now highly dependent on the management, curation and integration of large amounts of potentially useful data. Semantics are necessary in order to interpret the information and derive knowledge. Advances in recent years have mitigated concerns that the lack of robust, usable tools has inhibited the adoption of methodologies based on semantics. THIS PAPER PRESENTS THREE EXAMPLES OF HOW SEMANTIC WEB TECHNIQUES AND TECHNOLOGIES CAN BE USED IN ORDER TO SUPPORT CHEMISTRY RESEARCH: a controlled vocabulary for quantities, units and symbols in physical chemistry; a controlled vocabulary for the classification and labelling of chemical substances and mixtures; and, a database of chemical identifiers. This paper also presents a Web-based service that uses the datasets in order to assist with the completion of risk assessment forms, along with a discussion of the legal implications and value-proposition for the use of such a service. We have introduced the Semantic Web concepts, technologies, and methodologies that can be used to support chemistry research, and have demonstrated the application of those techniques in three areas very relevant to modern chemistry research, generating three new datasets that we offer as exemplars of an extensible portfolio of advanced data integration facilities. We have thereby established the importance of Semantic Web techniques and technologies for meeting Wild's fourth "grand challenge".

[Linked Data as a tool in the nutrition domain].

PubMed

Míguez Pérez, R; Santos Gago, J M; Alonso Rorís, V M; Álvarez Sabucedo, L M; Mikic Fonte, F A

2012-01-01

Currently, there is a huge amount of information available on Internet that can neither be interpreted nor used by software agents. This fact poses a serious drawback to the potential of tools that deal with data on the current Web. Nevertheless, in recent times, advances in the domain of Semantic Web make possible the development of a new generation of smart applications capable of creating added-value services for the final user. This work shows the technical challenges that must be faced in the area of nutrition in order to transform one or several oldfashion sources of raw data into a web repository based on semantic technologies and linked with external and publicly available data on Internet. This approach makes possible for automatic tools to operate on the top of this information providing new functionalities highly interesting in the domain of public health, such as the automatic generation of menus for children or intelligent dietetic assistants, among others. This article explains the process to create such information support applying the guidelines of the Linked Data initiative and provides insights into the use of tools to make the most of this technology for its adoption in related use cases and environments.

A Semantic Web-based System for Mining Genetic Mutations in Cancer Clinical Trials.

PubMed

Priya, Sambhawa; Jiang, Guoqian; Dasari, Surendra; Zimmermann, Michael T; Wang, Chen; Heflin, Jeff; Chute, Christopher G

2015-01-01

Textual eligibility criteria in clinical trial protocols contain important information about potential clinically relevant pharmacogenomic events. Manual curation for harvesting this evidence is intractable as it is error prone and time consuming. In this paper, we develop and evaluate a Semantic Web-based system that captures and manages mutation evidences and related contextual information from cancer clinical trials. The system has 2 main components: an NLP-based annotator and a Semantic Web ontology-based annotation manager. We evaluated the performance of the annotator in terms of precision and recall. We demonstrated the usefulness of the system by conducting case studies in retrieving relevant clinical trials using a collection of mutations identified from TCGA Leukemia patients and Atlas of Genetics and Cytogenetics in Oncology and Haematology. In conclusion, our system using Semantic Web technologies provides an effective framework for extraction, annotation, standardization and management of genetic mutations in cancer clinical trials.

Framework for Building Collaborative Research Environment

DOE PAGES

Devarakonda, Ranjeet; Palanisamy, Giriprakash; San Gil, Inigo

2014-10-25

Wide range of expertise and technologies are the key to solving some global problems. Semantic web technology can revolutionize the nature of how scientific knowledge is produced and shared. The semantic web is all about enabling machine-machine readability instead of a routine human-human interaction. Carefully structured data, as in machine readable data is the key to enabling these interactions. Drupal is an example of one such toolset that can render all the functionalities of Semantic Web technology right out of the box. Drupal’s content management system automatically stores the data in a structured format enabling it to be machine. Withinmore » this paper, we will discuss how Drupal promotes collaboration in a research setting such as Oak Ridge National Laboratory (ORNL) and Long Term Ecological Research Center (LTER) and how it is effectively using the Semantic Web in achieving this.« less

The semantic web and computer vision: old AI meets new AI

NASA Astrophysics Data System (ADS)

Mundy, J. L.; Dong, Y.; Gilliam, A.; Wagner, R.

2018-04-01

There has been vast process in linking semantic information across the billions of web pages through the use of ontologies encoded in the Web Ontology Language (OWL) based on the Resource Description Framework (RDF). A prime example is the Wikipedia where the knowledge contained in its more than four million pages is encoded in an ontological database called DBPedia http://wiki.dbpedia.org/. Web-based query tools can retrieve semantic information from DBPedia encoded in interlinked ontologies that can be accessed using natural language. This paper will show how this vast context can be used to automate the process of querying images and other geospatial data in support of report changes in structures and activities. Computer vision algorithms are selected and provided with context based on natural language requests for monitoring and analysis. The resulting reports provide semantically linked observations from images and 3D surface models.

Towards Web 3.0: taxonomies and ontologies for medical education -- a systematic review.

PubMed

Blaum, Wolf E; Jarczweski, Anne; Balzer, Felix; Stötzner, Philip; Ahlers, Olaf

2013-01-01

Both for curricular development and mapping, as well as for orientation within the mounting supply of learning resources in medical education, the Semantic Web ("Web 3.0") poses a low-threshold, effective tool that enables identification of content related items across system boundaries. Replacement of the currently required manual with an automatically generated link, which is based on content and semantics, requires the use of a suitably structured vocabulary for a machine-readable description of object content. Aim of this study is to compile the existing taxonomies and ontologies used for the annotation of medical content and learning resources, to compare those using selected criteria, and to verify their suitability in the context described above. Based on a systematic literature search, existing taxonomies and ontologies for the description of medical learning resources were identified. Through web searches and/or direct contact with the respective editors, each of the structured vocabularies thus identified were examined in regards to topic, structure, language, scope, maintenance, and technology of the taxonomy/ontology. In addition, suitability for use in the Semantic Web was verified. Among 20 identified publications, 14 structured vocabularies were identified, which differed rather strongly in regards to language, scope, currency, and maintenance. None of the identified vocabularies fulfilled the necessary criteria for content description of medical curricula and learning resources in the German-speaking world. While moving towards Web 3.0, a significant problem lies in the selection and use of an appropriate German vocabulary for the machine-readable description of object content. Possible solutions include development, translation and/or combination of existing vocabularies, possibly including partial translations of English vocabularies.

A journey to Semantic Web query federation in the life sciences.

PubMed

Cheung, Kei-Hoi; Frost, H Robert; Marshall, M Scott; Prud'hommeaux, Eric; Samwald, Matthias; Zhao, Jun; Paschke, Adrian

2009-10-01

As interest in adopting the Semantic Web in the biomedical domain continues to grow, Semantic Web technology has been evolving and maturing. A variety of technological approaches including triplestore technologies, SPARQL endpoints, Linked Data, and Vocabulary of Interlinked Datasets have emerged in recent years. In addition to the data warehouse construction, these technological approaches can be used to support dynamic query federation. As a community effort, the BioRDF task force, within the Semantic Web for Health Care and Life Sciences Interest Group, is exploring how these emerging approaches can be utilized to execute distributed queries across different neuroscience data sources. We have created two health care and life science knowledge bases. We have explored a variety of Semantic Web approaches to describe, map, and dynamically query multiple datasets. We have demonstrated several federation approaches that integrate diverse types of information about neurons and receptors that play an important role in basic, clinical, and translational neuroscience research. Particularly, we have created a prototype receptor explorer which uses OWL mappings to provide an integrated list of receptors and executes individual queries against different SPARQL endpoints. We have also employed the AIDA Toolkit, which is directed at groups of knowledge workers who cooperatively search, annotate, interpret, and enrich large collections of heterogeneous documents from diverse locations. We have explored a tool called "FeDeRate", which enables a global SPARQL query to be decomposed into subqueries against the remote databases offering either SPARQL or SQL query interfaces. Finally, we have explored how to use the vocabulary of interlinked Datasets (voiD) to create metadata for describing datasets exposed as Linked Data URIs or SPARQL endpoints. We have demonstrated the use of a set of novel and state-of-the-art Semantic Web technologies in support of a neuroscience query federation scenario. We have identified both the strengths and weaknesses of these technologies. While Semantic Web offers a global data model including the use of Uniform Resource Identifiers (URI's), the proliferation of semantically-equivalent URI's hinders large scale data integration. Our work helps direct research and tool development, which will be of benefit to this community.

A journey to Semantic Web query federation in the life sciences

PubMed Central

Cheung, Kei-Hoi; Frost, H Robert; Marshall, M Scott; Prud'hommeaux, Eric; Samwald, Matthias; Zhao, Jun; Paschke, Adrian

2009-01-01

Background As interest in adopting the Semantic Web in the biomedical domain continues to grow, Semantic Web technology has been evolving and maturing. A variety of technological approaches including triplestore technologies, SPARQL endpoints, Linked Data, and Vocabulary of Interlinked Datasets have emerged in recent years. In addition to the data warehouse construction, these technological approaches can be used to support dynamic query federation. As a community effort, the BioRDF task force, within the Semantic Web for Health Care and Life Sciences Interest Group, is exploring how these emerging approaches can be utilized to execute distributed queries across different neuroscience data sources. Methods and results We have created two health care and life science knowledge bases. We have explored a variety of Semantic Web approaches to describe, map, and dynamically query multiple datasets. We have demonstrated several federation approaches that integrate diverse types of information about neurons and receptors that play an important role in basic, clinical, and translational neuroscience research. Particularly, we have created a prototype receptor explorer which uses OWL mappings to provide an integrated list of receptors and executes individual queries against different SPARQL endpoints. We have also employed the AIDA Toolkit, which is directed at groups of knowledge workers who cooperatively search, annotate, interpret, and enrich large collections of heterogeneous documents from diverse locations. We have explored a tool called "FeDeRate", which enables a global SPARQL query to be decomposed into subqueries against the remote databases offering either SPARQL or SQL query interfaces. Finally, we have explored how to use the vocabulary of interlinked Datasets (voiD) to create metadata for describing datasets exposed as Linked Data URIs or SPARQL endpoints. Conclusion We have demonstrated the use of a set of novel and state-of-the-art Semantic Web technologies in support of a neuroscience query federation scenario. We have identified both the strengths and weaknesses of these technologies. While Semantic Web offers a global data model including the use of Uniform Resource Identifiers (URI's), the proliferation of semantically-equivalent URI's hinders large scale data integration. Our work helps direct research and tool development, which will be of benefit to this community. PMID:19796394

Dancing with the Web: Students Bring Meaning to the Semantic Web

ERIC Educational Resources Information Center

Brooks, Pauline

2012-01-01

This article will discuss the issues concerning the storage, retrieval and use of multimedia technology in dance, and how semantic web technologies can support those requirements. It will identify the key aims and outcomes of four international telematic dance projects, and review the use of reflective practice to engage students in their learning…

Populating the Semantic Web by Macro-reading Internet Text

NASA Astrophysics Data System (ADS)

Mitchell, Tom M.; Betteridge, Justin; Carlson, Andrew; Hruschka, Estevam; Wang, Richard

A key question regarding the future of the semantic web is "how will we acquire structured information to populate the semantic web on a vast scale?" One approach is to enter this information manually. A second approach is to take advantage of pre-existing databases, and to develop common ontologies, publishing standards, and reward systems to make this data widely accessible. We consider here a third approach: developing software that automatically extracts structured information from unstructured text present on the web. We also describe preliminary results demonstrating that machine learning algorithms can learn to extract tens of thousands of facts to populate a diverse ontology, with imperfect but reasonably good accuracy.

Biomedical question answering using semantic relations.

PubMed

Hristovski, Dimitar; Dinevski, Dejan; Kastrin, Andrej; Rindflesch, Thomas C

2015-01-16

The proliferation of the scientific literature in the field of biomedicine makes it difficult to keep abreast of current knowledge, even for domain experts. While general Web search engines and specialized information retrieval (IR) systems have made important strides in recent decades, the problem of accurate knowledge extraction from the biomedical literature is far from solved. Classical IR systems usually return a list of documents that have to be read by the user to extract relevant information. This tedious and time-consuming work can be lessened with automatic Question Answering (QA) systems, which aim to provide users with direct and precise answers to their questions. In this work we propose a novel methodology for QA based on semantic relations extracted from the biomedical literature. We extracted semantic relations with the SemRep natural language processing system from 122,421,765 sentences, which came from 21,014,382 MEDLINE citations (i.e., the complete MEDLINE distribution up to the end of 2012). A total of 58,879,300 semantic relation instances were extracted and organized in a relational database. The QA process is implemented as a search in this database, which is accessed through a Web-based application, called SemBT (available at http://sembt.mf.uni-lj.si ). We conducted an extensive evaluation of the proposed methodology in order to estimate the accuracy of extracting a particular semantic relation from a particular sentence. Evaluation was performed by 80 domain experts. In total 7,510 semantic relation instances belonging to 2,675 distinct relations were evaluated 12,083 times. The instances were evaluated as correct 8,228 times (68%). In this work we propose an innovative methodology for biomedical QA. The system is implemented as a Web-based application that is able to provide precise answers to a wide range of questions. A typical question is answered within a few seconds. The tool has some extensions that make it especially useful for interpretation of DNA microarray results.

Semantic Advertising for Web 3.0

NASA Astrophysics Data System (ADS)

Thomas, Edward; Pan, Jeff Z.; Taylor, Stuart; Ren, Yuan; Jekjantuk, Nophadol; Zhao, Yuting

Advertising on the World Wide Web is based around automatically matching web pages with appropriate advertisements, in the form of banner ads, interactive adverts, or text links. Traditionally this has been done by manual classification of pages, or more recently using information retrieval techniques to find the most important keywords from the page, and match these to keywords being used by adverts. In this paper, we propose a new model for online advertising, based around lightweight embedded semantics. This will improve the relevancy of adverts on the World Wide Web and help to kick-start the use of RDFa as a mechanism for adding lightweight semantic attributes to the Web. Furthermore, we propose a system architecture for the proposed new model, based on our scalable ontology reasoning infrastructure TrOWL.

Ontology Design of Influential People Identification Using Centrality

NASA Astrophysics Data System (ADS)

Maulana Awangga, Rolly; Yusril, Muhammad; Setyawan, Helmi

2018-04-01

Identifying influential people as a node in a graph theory commonly calculated by social network analysis. The social network data has the user as node and edge as relation forming a friend relation graph. This research is conducting different meaning of every nodes relation in the social network. Ontology was perfect match science to describe the social network data as conceptual and domain. Ontology gives essential relationship in a social network more than a current graph. Ontology proposed as a standard for knowledge representation for the semantic web by World Wide Web Consortium. The formal data representation use Resource Description Framework (RDF) and Web Ontology Language (OWL) which is strategic for Open Knowledge-Based website data. Ontology used in the semantic description for a relationship in the social network, it is open to developing semantic based relationship ontology by adding and modifying various and different relationship to have influential people as a conclusion. This research proposes a model using OWL and RDF for influential people identification in the social network. The study use degree centrality, between ness centrality, and closeness centrality measurement for data validation. As a conclusion, influential people identification in Facebook can use proposed Ontology model in the Group, Photos, Photo Tag, Friends, Events and Works data.

c-Mantic: A Cytoscape plugin for Semantic Web

EPA Science Inventory

Semantic Web tools can streamline the process of storing, analyzing and sharing biological information. Visualization is important for communicating such complex biological relationships. Here we use the flexibility and speed of the Cytoscape platform to interactively visualize s...

Semantic Annotations and Querying of Web Data Sources

NASA Astrophysics Data System (ADS)

Hornung, Thomas; May, Wolfgang

A large part of the Web, actually holding a significant portion of the useful information throughout the Web, consists of views on hidden databases, provided by numerous heterogeneous interfaces that are partly human-oriented via Web forms ("Deep Web"), and partly based on Web Services (only machine accessible). In this paper we present an approach for annotating these sources in a way that makes them citizens of the Semantic Web. We illustrate how queries can be stated in terms of the ontology, and how the annotations are used to selected and access appropriate sources and to answer the queries.

Linked Data: what does it offer Earth Sciences?

NASA Astrophysics Data System (ADS)

Cox, Simon; Schade, Sven

2010-05-01

'Linked Data' is a current buzz-phrase promoting access to various forms of data on the internet. It starts from the two principles that have underpinned the architecture and scalability of the World Wide Web: 1. Universal Resource Identifiers - using the http protocol which is supported by the DNS system. 2. Hypertext - in which URIs of related resources are embedded within a document. Browsing is the key mode of interaction, with traversal of links between resources under control of the client. Linked Data also adds, or re-emphasizes: • Content negotiation - whereby the client uses http headers to tell the service what representation of a resource is acceptable, • Semantic Web principles - formal semantics for links, following the RDF data model and encoding, and • The 'mashup' effect - in which original and unexpected value may emerge from reuse of data, even if published in raw or unpolished form. Linked Data promotes typed links to all kinds of data, so is where the semantic web meets the 'deep web', i.e. resources which may be accessed using web protocols, but are in representations not indexed by search engines. Earth sciences are data rich, but with a strong legacy of specialized formats managed and processed by disconnected applications. However, most contemporary research problems require a cross-disciplinary approach, in which the heterogeneity resulting from that legacy is a significant challenge. In this context, Linked Data clearly has much to offer the earth sciences. But, there are some important questions to answer. What is a resource? Most earth science data is organized in arrays and databases. A subset useful for a particular study is usually identified by a parameterized query. The Linked Data paradigm emerged from the world of documents, and will often only resolve data-sets. It is impractical to create even nested navigation resources containing links to all potentially useful objects or subsets. From the viewpoint of human user interfaces, the browse metaphor, which has been such an important part of the success of the web, must be augmented with other interaction mechanisms, including query. What are the impacts on search and metadata? Hypertext provides links selected by the page provider. However, science should endeavor to be exhaustive in its use of data. Resource discovery through links must be supplemented by more systematic data discovery through search. Conversely, the crawlers that generate search indexes must be fed by resource providers (a) serving navigation pages with links to every dataset (b) adding enough 'metadata' (semantics) on each link to effectively populate the indexes. Linked Data makes this easier due to its integration with semantic web technologies, including structured vocabularies. What is the relation between structured data and Linked Data? Linked Data has focused on web-pages (primarily HTML) for human browsing, and RDF for semantics, assuming that other representations are opaque. However, this overlooks the wealth of XML data on the web, some of which is structured according to XML Schemas that provide semantics. Technical applications can use content-negotiation to get a structured representation, and exploit its semantics. Particularly relevant for earth sciences are data representations based on OGC Geography Markup Language (GML), such as GeoSciML, O&M and MOLES. GML was strongly influenced by RDF, and typed links are intrinsic: xlink:href plays the role that rdf:resource does in RDF representations. Services which expose GML-formatted resources (such as OGC Web Feature Service) are a prototype of Linked Data. Giving credit where it is due. Organizations investing in data collection may be reluctant to publish the raw data prior to completing an initial analysis. To encourage early data publication the system must provide suitable incentives, and citation analysis must recognize the increasing diversity of publication routes and forms. Linked Data makes it easier to include rich citation information when data is both published and used.

Developing an Ontology for Ocean Biogeochemistry Data

NASA Astrophysics Data System (ADS)

Chandler, C. L.; Allison, M. D.; Groman, R. C.; West, P.; Zednik, S.; Maffei, A. R.

2010-12-01

Semantic Web technologies offer great promise for enabling new and better scientific research. However, significant challenges must be met before the promise of the Semantic Web can be realized for a discipline as diverse as oceanography. Evolving expectations for open access to research data combined with the complexity of global ecosystem science research themes present a significant challenge, and one that is best met through an informatics approach. The Biological and Chemical Oceanography Data Management Office (BCO-DMO) is funded by the National Science Foundation Division of Ocean Sciences to work with ocean biogeochemistry researchers to improve access to data resulting from their respective programs. In an effort to improve data access, BCO-DMO staff members are collaborating with researchers from the Tetherless World Constellation (Rensselaer Polytechnic Institute) to develop an ontology that formally describes the concepts and relationships in the data managed by the BCO-DMO. The project required transforming a legacy system of human-readable, flat files of metadata to well-ordered controlled vocabularies to a fully developed ontology. To improve semantic interoperability, terms from the BCO-DMO controlled vocabularies are being mapped to controlled vocabulary terms adopted by other oceanographic data management organizations. While the entire process has proven to be difficult, time-consuming and labor-intensive, the work has been rewarding and is a necessary prerequisite for the eventual incorporation of Semantic Web tools. From the beginning of the project, development of the ontology has been guided by a use case based approach. The use cases were derived from data access related requests received from members of the research community served by the BCO-DMO. The resultant ontology satisfies the requirements of the use cases and reflects the information stored in the metadata database. The BCO-DMO metadata database currently contains information that powers several different user and machine-to-machine interfaces to the BCO-DMO data repositories. One goal of the ontology development project is to enable subsequent development of semantically-enabled components (e.g. faceted search) to enhance the power of those interfaces. Addition of semantic capabilities to the existing data interfaces will improve data access through enhanced data discovery. In addition to sharing the ontology, we will describe the challenges encountered thus far in the project, the technologies currently being used, and the strategies associated with the use case based informatics approach.

An Ontology of Quality Initiatives and a Model for Decentralized, Collaborative Quality Management on the (Semantic) World Wide Web

PubMed Central

2001-01-01

This editorial provides a model of how quality initiatives concerned with health information on the World Wide Web may in the future interact with each other. This vision fits into the evolving "Semantic Web" architecture - ie, the prospective that the World Wide Web may evolve from a mess of unstructured, human-readable information sources into a global knowledge base with an additional layer providing richer and more meaningful relationships between resources. One first prerequisite for forming such a "Semantic Web" or "web of trust" among the players active in quality management of health information is that these initiatives make statements about themselves and about each other in a machine-processable language. I present a concrete model on how this collaboration could look, and provide some recommendations on what the role of the World Health Organization (WHO) and other policy makers in this framework could be. PMID:11772549

An ontology of quality initiatives and a model for decentralized, collaborative quality management on the (semantic) World-Wide-Web.

PubMed

Eysenbach, G

2001-01-01

This editorial provides a model of how quality initiatives concerned with health information on the World Wide Web may in the future interact with each other. This vision fits into the evolving "Semantic Web" architecture - ie, the prospective that the World Wide Web may evolve from a mess of unstructured, human-readable information sources into a global knowledge base with an additional layer providing richer and more meaningful relationships between resources. One first prerequisite for forming such a "Semantic Web" or "web of trust" among the players active in quality management of health information is that these initiatives make statements about themselves and about each other in a machine-processable language. I present a concrete model on how this collaboration could look, and provide some recommendations on what the role of the World Health Organization (WHO) and other policy makers in this framework could be.

Towards an Approach of Semantic Access Control for Cloud Computing

NASA Astrophysics Data System (ADS)

Hu, Luokai; Ying, Shi; Jia, Xiangyang; Zhao, Kai

With the development of cloud computing, the mutual understandability among distributed Access Control Policies (ACPs) has become an important issue in the security field of cloud computing. Semantic Web technology provides the solution to semantic interoperability of heterogeneous applications. In this paper, we analysis existing access control methods and present a new Semantic Access Control Policy Language (SACPL) for describing ACPs in cloud computing environment. Access Control Oriented Ontology System (ACOOS) is designed as the semantic basis of SACPL. Ontology-based SACPL language can effectively solve the interoperability issue of distributed ACPs. This study enriches the research that the semantic web technology is applied in the field of security, and provides a new way of thinking of access control in cloud computing.

SemanticOrganizer: A Customizable Semantic Repository for Distributed NASA Project Teams

NASA Technical Reports Server (NTRS)

Keller, Richard M.; Berrios, Daniel C.; Carvalho, Robert E.; Hall, David R.; Rich, Stephen J.; Sturken, Ian B.; Swanson, Keith J.; Wolfe, Shawn R.

2004-01-01

SemanticOrganizer is a collaborative knowledge management system designed to support distributed NASA projects, including diverse teams of scientists, engineers, and accident investigators. The system provides a customizable, semantically structured information repository that stores work products relevant to multiple projects of differing types. SemanticOrganizer is one of the earliest and largest semantic web applications deployed at NASA to date, and has been used in diverse contexts ranging from the investigation of Space Shuttle Columbia's accident to the search for life on other planets. Although the underlying repository employs a single unified ontology, access control and ontology customization mechanisms make the repository contents appear different for each project team. This paper describes SemanticOrganizer, its customization facilities, and a sampling of its applications. The paper also summarizes some key lessons learned from building and fielding a successful semantic web application across a wide-ranging set of domains with diverse users.

Using Semantic Web technologies for the generation of domain-specific templates to support clinical study metadata standards.

PubMed

Jiang, Guoqian; Evans, Julie; Endle, Cory M; Solbrig, Harold R; Chute, Christopher G

2016-01-01

The Biomedical Research Integrated Domain Group (BRIDG) model is a formal domain analysis model for protocol-driven biomedical research, and serves as a semantic foundation for application and message development in the standards developing organizations (SDOs). The increasing sophistication and complexity of the BRIDG model requires new approaches to the management and utilization of the underlying semantics to harmonize domain-specific standards. The objective of this study is to develop and evaluate a Semantic Web-based approach that integrates the BRIDG model with ISO 21090 data types to generate domain-specific templates to support clinical study metadata standards development. We developed a template generation and visualization system based on an open source Resource Description Framework (RDF) store backend, a SmartGWT-based web user interface, and a "mind map" based tool for the visualization of generated domain-specific templates. We also developed a RESTful Web Service informed by the Clinical Information Modeling Initiative (CIMI) reference model for access to the generated domain-specific templates. A preliminary usability study is performed and all reviewers (n = 3) had very positive responses for the evaluation questions in terms of the usability and the capability of meeting the system requirements (with the average score of 4.6). Semantic Web technologies provide a scalable infrastructure and have great potential to enable computable semantic interoperability of models in the intersection of health care and clinical research.

Semantically-enabled sensor plug & play for the sensor web.

PubMed

Bröring, Arne; Maúe, Patrick; Janowicz, Krzysztof; Nüst, Daniel; Malewski, Christian

2011-01-01

Environmental sensors have continuously improved by becoming smaller, cheaper, and more intelligent over the past years. As consequence of these technological advancements, sensors are increasingly deployed to monitor our environment. The large variety of available sensor types with often incompatible protocols complicates the integration of sensors into observing systems. The standardized Web service interfaces and data encodings defined within OGC's Sensor Web Enablement (SWE) framework make sensors available over the Web and hide the heterogeneous sensor protocols from applications. So far, the SWE framework does not describe how to integrate sensors on-the-fly with minimal human intervention. The driver software which enables access to sensors has to be implemented and the measured sensor data has to be manually mapped to the SWE models. In this article we introduce a Sensor Plug & Play infrastructure for the Sensor Web by combining (1) semantic matchmaking functionality, (2) a publish/subscribe mechanism underlying the SensorWeb, as well as (3) a model for the declarative description of sensor interfaces which serves as a generic driver mechanism. We implement and evaluate our approach by applying it to an oil spill scenario. The matchmaking is realized using existing ontologies and reasoning engines and provides a strong case for the semantic integration capabilities provided by Semantic Web research.

Semantically-Enabled Sensor Plug & Play for the Sensor Web

PubMed Central

Bröring, Arne; Maúe, Patrick; Janowicz, Krzysztof; Nüst, Daniel; Malewski, Christian

2011-01-01

Environmental sensors have continuously improved by becoming smaller, cheaper, and more intelligent over the past years. As consequence of these technological advancements, sensors are increasingly deployed to monitor our environment. The large variety of available sensor types with often incompatible protocols complicates the integration of sensors into observing systems. The standardized Web service interfaces and data encodings defined within OGC’s Sensor Web Enablement (SWE) framework make sensors available over the Web and hide the heterogeneous sensor protocols from applications. So far, the SWE framework does not describe how to integrate sensors on-the-fly with minimal human intervention. The driver software which enables access to sensors has to be implemented and the measured sensor data has to be manually mapped to the SWE models. In this article we introduce a Sensor Plug & Play infrastructure for the Sensor Web by combining (1) semantic matchmaking functionality, (2) a publish/subscribe mechanism underlying the SensorWeb, as well as (3) a model for the declarative description of sensor interfaces which serves as a generic driver mechanism. We implement and evaluate our approach by applying it to an oil spill scenario. The matchmaking is realized using existing ontologies and reasoning engines and provides a strong case for the semantic integration capabilities provided by Semantic Web research. PMID:22164033

A Semantic Sensor Web for Environmental Decision Support Applications

PubMed Central

Gray, Alasdair J. G.; Sadler, Jason; Kit, Oles; Kyzirakos, Kostis; Karpathiotakis, Manos; Calbimonte, Jean-Paul; Page, Kevin; García-Castro, Raúl; Frazer, Alex; Galpin, Ixent; Fernandes, Alvaro A. A.; Paton, Norman W.; Corcho, Oscar; Koubarakis, Manolis; De Roure, David; Martinez, Kirk; Gómez-Pérez, Asunción

2011-01-01

Sensing devices are increasingly being deployed to monitor the physical world around us. One class of application for which sensor data is pertinent is environmental decision support systems, e.g., flood emergency response. For these applications, the sensor readings need to be put in context by integrating them with other sources of data about the surrounding environment. Traditional systems for predicting and detecting floods rely on methods that need significant human resources. In this paper we describe a semantic sensor web architecture for integrating multiple heterogeneous datasets, including live and historic sensor data, databases, and map layers. The architecture provides mechanisms for discovering datasets, defining integrated views over them, continuously receiving data in real-time, and visualising on screen and interacting with the data. Our approach makes extensive use of web service standards for querying and accessing data, and semantic technologies to discover and integrate datasets. We demonstrate the use of our semantic sensor web architecture in the context of a flood response planning web application that uses data from sensor networks monitoring the sea-state around the coast of England. PMID:22164110

Semantic annotation of consumer health questions.

PubMed

Kilicoglu, Halil; Ben Abacha, Asma; Mrabet, Yassine; Shooshan, Sonya E; Rodriguez, Laritza; Masterton, Kate; Demner-Fushman, Dina

2018-02-06

Consumers increasingly use online resources for their health information needs. While current search engines can address these needs to some extent, they generally do not take into account that most health information needs are complex and can only fully be expressed in natural language. Consumer health question answering (QA) systems aim to fill this gap. A major challenge in developing consumer health QA systems is extracting relevant semantic content from the natural language questions (question understanding). To develop effective question understanding tools, question corpora semantically annotated for relevant question elements are needed. In this paper, we present a two-part consumer health question corpus annotated with several semantic categories: named entities, question triggers/types, question frames, and question topic. The first part (CHQA-email) consists of relatively long email requests received by the U.S. National Library of Medicine (NLM) customer service, while the second part (CHQA-web) consists of shorter questions posed to MedlinePlus search engine as queries. Each question has been annotated by two annotators. The annotation methodology is largely the same between the two parts of the corpus; however, we also explain and justify the differences between them. Additionally, we provide information about corpus characteristics, inter-annotator agreement, and our attempts to measure annotation confidence in the absence of adjudication of annotations. The resulting corpus consists of 2614 questions (CHQA-email: 1740, CHQA-web: 874). Problems are the most frequent named entities, while treatment and general information questions are the most common question types. Inter-annotator agreement was generally modest: question types and topics yielded highest agreement, while the agreement for more complex frame annotations was lower. Agreement in CHQA-web was consistently higher than that in CHQA-email. Pairwise inter-annotator agreement proved most useful in estimating annotation confidence. To our knowledge, our corpus is the first focusing on annotation of uncurated consumer health questions. It is currently used to develop machine learning-based methods for question understanding. We make the corpus publicly available to stimulate further research on consumer health QA.

BioUSeR: a semantic-based tool for retrieving Life Science web resources driven by text-rich user requirements

PubMed Central

2013-01-01

Background Open metadata registries are a fundamental tool for researchers in the Life Sciences trying to locate resources. While most current registries assume that resources are annotated with well-structured metadata, evidence shows that most of the resource annotations simply consists of informal free text. This reality must be taken into account in order to develop effective techniques for resource discovery in Life Sciences. Results BioUSeR is a semantic-based tool aimed at retrieving Life Sciences resources described in free text. The retrieval process is driven by the user requirements, which consist of a target task and a set of facets of interest, both expressed in free text. BioUSeR is able to effectively exploit the available textual descriptions to find relevant resources by using semantic-aware techniques. Conclusions BioUSeR overcomes the limitations of the current registries thanks to: (i) rich specification of user information needs, (ii) use of semantics to manage textual descriptions, (iii) retrieval and ranking of resources based on user requirements. PMID:23635042

Ontology Research and Development. Part 1-A Review of Ontology Generation.

ERIC Educational Resources Information Center

Ding, Ying; Foo, Schubert

2002-01-01

Discusses the role of ontology in knowledge representation, including enabling content-based access, interoperability, communications, and new levels of service on the Semantic Web; reviews current ontology generation studies and projects as well as problems facing such research; and discusses ontology mapping, information extraction, natural…

A Methodology for Enhancing Mobile Learning through Content Semantics

ERIC Educational Resources Information Center

Dimitrios, Glaroudis; Athanasios, Manitsaris; Isabella, Kotini

2013-01-01

Mobile learning is becoming increasingly popular. Educational web sites can be used as supporting learning tools for students who wish to supplement their knowledge without restrictions of time and place. The continuously increasing demand for enhanced remote and mobile services, as well as the difficulty in easily incorporating current learning…

A Methodology for the Development of RESTful Semantic Web Services for Gene Expression Analysis

PubMed Central

Guardia, Gabriela D. A.; Pires, Luís Ferreira; Vêncio, Ricardo Z. N.; Malmegrim, Kelen C. R.; de Farias, Cléver R. G.

2015-01-01

Gene expression studies are generally performed through multi-step analysis processes, which require the integrated use of a number of analysis tools. In order to facilitate tool/data integration, an increasing number of analysis tools have been developed as or adapted to semantic web services. In recent years, some approaches have been defined for the development and semantic annotation of web services created from legacy software tools, but these approaches still present many limitations. In addition, to the best of our knowledge, no suitable approach has been defined for the functional genomics domain. Therefore, this paper aims at defining an integrated methodology for the implementation of RESTful semantic web services created from gene expression analysis tools and the semantic annotation of such services. We have applied our methodology to the development of a number of services to support the analysis of different types of gene expression data, including microarray and RNASeq. All developed services are publicly available in the Gene Expression Analysis Services (GEAS) Repository at http://dcm.ffclrp.usp.br/lssb/geas. Additionally, we have used a number of the developed services to create different integrated analysis scenarios to reproduce parts of two gene expression studies documented in the literature. The first study involves the analysis of one-color microarray data obtained from multiple sclerosis patients and healthy donors. The second study comprises the analysis of RNA-Seq data obtained from melanoma cells to investigate the role of the remodeller BRG1 in the proliferation and morphology of these cells. Our methodology provides concrete guidelines and technical details in order to facilitate the systematic development of semantic web services. Moreover, it encourages the development and reuse of these services for the creation of semantically integrated solutions for gene expression analysis. PMID:26207740

The Semantic Web: From Representation to Realization

NASA Astrophysics Data System (ADS)

Thórisson, Kristinn R.; Spivack, Nova; Wissner, James M.

A semantically-linked web of electronic information - the Semantic Web - promises numerous benefits including increased precision in automated information sorting, searching, organizing and summarizing. Realizing this requires significantly more reliable meta-information than is readily available today. It also requires a better way to represent information that supports unified management of diverse data and diverse Manipulation methods: from basic keywords to various types of artificial intelligence, to the highest level of intelligent manipulation - the human mind. How this is best done is far from obvious. Relying solely on hand-crafted annotation and ontologies, or solely on artificial intelligence techniques, seems less likely for success than a combination of the two. In this paper describe an integrated, complete solution to these challenges that has already been implemented and tested with hundreds of thousands of users. It is based on an ontological representational level we call SemCards that combines ontological rigour with flexible user interface constructs. SemCards are machine- and human-readable digital entities that allow non-experts to create and use semantic content, while empowering machines to better assist and participate in the process. SemCards enable users to easily create semantically-grounded data that in turn acts as examples for automation processes, creating a positive iterative feedback loop of metadata creation and refinement between user and machine. They provide a holistic solution to the Semantic Web, supporting powerful management of the full lifecycle of data, including its creation, retrieval, classification, sorting and sharing. We have implemented the SemCard technology on the semantic Web site Twine.com, showing that the technology is indeed versatile and scalable. Here we present the key ideas behind SemCards and describe the initial implementation of the technology.

A Methodology for the Development of RESTful Semantic Web Services for Gene Expression Analysis.

PubMed

Guardia, Gabriela D A; Pires, Luís Ferreira; Vêncio, Ricardo Z N; Malmegrim, Kelen C R; de Farias, Cléver R G

2015-01-01

Gene expression studies are generally performed through multi-step analysis processes, which require the integrated use of a number of analysis tools. In order to facilitate tool/data integration, an increasing number of analysis tools have been developed as or adapted to semantic web services. In recent years, some approaches have been defined for the development and semantic annotation of web services created from legacy software tools, but these approaches still present many limitations. In addition, to the best of our knowledge, no suitable approach has been defined for the functional genomics domain. Therefore, this paper aims at defining an integrated methodology for the implementation of RESTful semantic web services created from gene expression analysis tools and the semantic annotation of such services. We have applied our methodology to the development of a number of services to support the analysis of different types of gene expression data, including microarray and RNASeq. All developed services are publicly available in the Gene Expression Analysis Services (GEAS) Repository at http://dcm.ffclrp.usp.br/lssb/geas. Additionally, we have used a number of the developed services to create different integrated analysis scenarios to reproduce parts of two gene expression studies documented in the literature. The first study involves the analysis of one-color microarray data obtained from multiple sclerosis patients and healthy donors. The second study comprises the analysis of RNA-Seq data obtained from melanoma cells to investigate the role of the remodeller BRG1 in the proliferation and morphology of these cells. Our methodology provides concrete guidelines and technical details in order to facilitate the systematic development of semantic web services. Moreover, it encourages the development and reuse of these services for the creation of semantically integrated solutions for gene expression analysis.

Semantic framework for mapping object-oriented model to semantic web languages

PubMed Central

Ježek, Petr; Mouček, Roman

2015-01-01

The article deals with and discusses two main approaches in building semantic structures for electrophysiological metadata. It is the use of conventional data structures, repositories, and programming languages on one hand and the use of formal representations of ontologies, known from knowledge representation, such as description logics or semantic web languages on the other hand. Although knowledge engineering offers languages supporting richer semantic means of expression and technological advanced approaches, conventional data structures and repositories are still popular among developers, administrators and users because of their simplicity, overall intelligibility, and lower demands on technical equipment. The choice of conventional data resources and repositories, however, raises the question of how and where to add semantics that cannot be naturally expressed using them. As one of the possible solutions, this semantics can be added into the structures of the programming language that accesses and processes the underlying data. To support this idea we introduced a software prototype that enables its users to add semantically richer expressions into a Java object-oriented code. This approach does not burden users with additional demands on programming environment since reflective Java annotations were used as an entry for these expressions. Moreover, additional semantics need not to be written by the programmer directly to the code, but it can be collected from non-programmers using a graphic user interface. The mapping that allows the transformation of the semantically enriched Java code into the Semantic Web language OWL was proposed and implemented in a library named the Semantic Framework. This approach was validated by the integration of the Semantic Framework in the EEG/ERP Portal and by the subsequent registration of the EEG/ERP Portal in the Neuroscience Information Framework. PMID:25762923

Semantic framework for mapping object-oriented model to semantic web languages.

PubMed

Ježek, Petr; Mouček, Roman

2015-01-01

The article deals with and discusses two main approaches in building semantic structures for electrophysiological metadata. It is the use of conventional data structures, repositories, and programming languages on one hand and the use of formal representations of ontologies, known from knowledge representation, such as description logics or semantic web languages on the other hand. Although knowledge engineering offers languages supporting richer semantic means of expression and technological advanced approaches, conventional data structures and repositories are still popular among developers, administrators and users because of their simplicity, overall intelligibility, and lower demands on technical equipment. The choice of conventional data resources and repositories, however, raises the question of how and where to add semantics that cannot be naturally expressed using them. As one of the possible solutions, this semantics can be added into the structures of the programming language that accesses and processes the underlying data. To support this idea we introduced a software prototype that enables its users to add semantically richer expressions into a Java object-oriented code. This approach does not burden users with additional demands on programming environment since reflective Java annotations were used as an entry for these expressions. Moreover, additional semantics need not to be written by the programmer directly to the code, but it can be collected from non-programmers using a graphic user interface. The mapping that allows the transformation of the semantically enriched Java code into the Semantic Web language OWL was proposed and implemented in a library named the Semantic Framework. This approach was validated by the integration of the Semantic Framework in the EEG/ERP Portal and by the subsequent registration of the EEG/ERP Portal in the Neuroscience Information Framework.

The Power and Peril of Web 3.0: It's More than Just Semantics

ERIC Educational Resources Information Center

Ohler, Jason

2010-01-01

The Information Age has been built, in part, on the belief that more information is always better. True to that sentiment, people have found ways to make a lot of information available to the masses--perhaps more than anyone ever imagined. The goal of the Semantic Web, often called Web 3.0, is for users to spend less time looking for information…

Web Video Event Recognition by Semantic Analysis From Ubiquitous Documents.

PubMed

Yu, Litao; Yang, Yang; Huang, Zi; Wang, Peng; Song, Jingkuan; Shen, Heng Tao

2016-12-01

In recent years, the task of event recognition from videos has attracted increasing interest in multimedia area. While most of the existing research was mainly focused on exploring visual cues to handle relatively small-granular events, it is difficult to directly analyze video content without any prior knowledge. Therefore, synthesizing both the visual and semantic analysis is a natural way for video event understanding. In this paper, we study the problem of Web video event recognition, where Web videos often describe large-granular events and carry limited textual information. Key challenges include how to accurately represent event semantics from incomplete textual information and how to effectively explore the correlation between visual and textual cues for video event understanding. We propose a novel framework to perform complex event recognition from Web videos. In order to compensate the insufficient expressive power of visual cues, we construct an event knowledge base by deeply mining semantic information from ubiquitous Web documents. This event knowledge base is capable of describing each event with comprehensive semantics. By utilizing this base, the textual cues for a video can be significantly enriched. Furthermore, we introduce a two-view adaptive regression model, which explores the intrinsic correlation between the visual and textual cues of the videos to learn reliable classifiers. Extensive experiments on two real-world video data sets show the effectiveness of our proposed framework and prove that the event knowledge base indeed helps improve the performance of Web video event recognition.

Students as Designers of Semantic Web Applications

ERIC Educational Resources Information Center

Tracy, Fran; Jordan, Katy

2012-01-01

This paper draws upon the experience of an interdisciplinary research group in engaging undergraduate university students in the design and development of semantic web technologies. A flexible approach to participatory design challenged conventional distinctions between "designer" and "user" and allowed students to play a role…

Cases, Simulacra, and Semantic Web Technologies

ERIC Educational Resources Information Center

Carmichael, P.; Tscholl, M.

2013-01-01

"Ensemble" is an interdisciplinary research and development project exploring the potential role of emerging Semantic Web technologies in case-based learning across learning environments in higher education. Empirical findings have challenged the claim that cases "bring reality into the classroom" and that this, in turn, might…

A case study of data integration for aquatic resources using semantic web technologies

USGS Publications Warehouse

Gordon, Janice M.; Chkhenkeli, Nina; Govoni, David L.; Lightsom, Frances L.; Ostroff, Andrea C.; Schweitzer, Peter N.; Thongsavanh, Phethala; Varanka, Dalia E.; Zednik, Stephan

2015-01-01

Use cases, information modeling, and linked data techniques are Semantic Web technologies used to develop a prototype system that integrates scientific observations from four independent USGS and cooperator data systems. The techniques were tested with a use case goal of creating a data set for use in exploring potential relationships among freshwater fish populations and environmental factors. The resulting prototype extracts data from the BioData Retrieval System, the Multistate Aquatic Resource Information System, the National Geochemical Survey, and the National Hydrography Dataset. A prototype user interface allows a scientist to select observations from these data systems and combine them into a single data set in RDF format that includes explicitly defined relationships and data definitions. The project was funded by the USGS Community for Data Integration and undertaken by the Community for Data Integration Semantic Web Working Group in order to demonstrate use of Semantic Web technologies by scientists. This allows scientists to simultaneously explore data that are available in multiple, disparate systems beyond those they traditionally have used.

CASAS: A tool for composing automatically and semantically astrophysical services

NASA Astrophysics Data System (ADS)

Louge, T.; Karray, M. H.; Archimède, B.; Knödlseder, J.

2017-07-01

Multiple astronomical datasets are available through internet and the astrophysical Distributed Computing Infrastructure (DCI) called Virtual Observatory (VO). Some scientific workflow technologies exist for retrieving and combining data from those sources. However selection of relevant services, automation of the workflows composition and the lack of user-friendly platforms remain a concern. This paper presents CASAS, a tool for semantic web services composition in astrophysics. This tool proposes automatic composition of astrophysical web services and brings a semantics-based, automatic composition of workflows. It widens the services choice and eases the use of heterogeneous services. Semantic web services composition relies on ontologies for elaborating the services composition; this work is based on Astrophysical Services ONtology (ASON). ASON had its structure mostly inherited from the VO services capacities. Nevertheless, our approach is not limited to the VO and brings VO plus non-VO services together without the need for premade recipes. CASAS is available for use through a simple web interface.

Semantic Similarity between Web Documents Using Ontology

NASA Astrophysics Data System (ADS)

Chahal, Poonam; Singh Tomer, Manjeet; Kumar, Suresh

2018-06-01

The World Wide Web is the source of information available in the structure of interlinked web pages. However, the procedure of extracting significant information with the assistance of search engine is incredibly critical. This is for the reason that web information is written mainly by using natural language, and further available to individual human. Several efforts have been made in semantic similarity computation between documents using words, concepts and concepts relationship but still the outcome available are not as per the user requirements. This paper proposes a novel technique for computation of semantic similarity between documents that not only takes concepts available in documents but also relationships that are available between the concepts. In our approach documents are being processed by making ontology of the documents using base ontology and a dictionary containing concepts records. Each such record is made up of the probable words which represents a given concept. Finally, document ontology's are compared to find their semantic similarity by taking the relationships among concepts. Relevant concepts and relations between the concepts have been explored by capturing author and user intention. The proposed semantic analysis technique provides improved results as compared to the existing techniques.

Semantic Similarity between Web Documents Using Ontology

NASA Astrophysics Data System (ADS)

Chahal, Poonam; Singh Tomer, Manjeet; Kumar, Suresh

2018-03-01

The World Wide Web is the source of information available in the structure of interlinked web pages. However, the procedure of extracting significant information with the assistance of search engine is incredibly critical. This is for the reason that web information is written mainly by using natural language, and further available to individual human. Several efforts have been made in semantic similarity computation between documents using words, concepts and concepts relationship but still the outcome available are not as per the user requirements. This paper proposes a novel technique for computation of semantic similarity between documents that not only takes concepts available in documents but also relationships that are available between the concepts. In our approach documents are being processed by making ontology of the documents using base ontology and a dictionary containing concepts records. Each such record is made up of the probable words which represents a given concept. Finally, document ontology's are compared to find their semantic similarity by taking the relationships among concepts. Relevant concepts and relations between the concepts have been explored by capturing author and user intention. The proposed semantic analysis technique provides improved results as compared to the existing techniques.

Using RDF to Model the Structure and Process of Systems

NASA Astrophysics Data System (ADS)

Rodriguez, Marko A.; Watkins, Jennifer H.; Bollen, Johan; Gershenson, Carlos

Many systems can be described in terms of networks of discrete elements and their various relationships to one another. A semantic network, or multi-relational network, is a directed labeled graph consisting of a heterogeneous set of entities connected by a heterogeneous set of relationships. Semantic networks serve as a promising general-purpose modeling substrate for complex systems. Various standardized formats and tools are now available to support practical, large-scale semantic network models. First, the Resource Description Framework (RDF) offers a standardized semantic network data model that can be further formalized by ontology modeling languages such as RDF Schema (RDFS) and the Web Ontology Language (OWL). Second, the recent introduction of highly performant triple-stores (i.e. semantic network databases) allows semantic network models on the order of 109 edges to be efficiently stored and manipulated. RDF and its related technologies are currently used extensively in the domains of computer science, digital library science, and the biological sciences. This article will provide an introduction to RDF/RDFS/OWL and an examination of its suitability to model discrete element complex systems.

A semantic web framework to integrate cancer omics data with biological knowledge.

PubMed

Holford, Matthew E; McCusker, James P; Cheung, Kei-Hoi; Krauthammer, Michael

2012-01-25

The RDF triple provides a simple linguistic means of describing limitless types of information. Triples can be flexibly combined into a unified data source we call a semantic model. Semantic models open new possibilities for the integration of variegated biological data. We use Semantic Web technology to explicate high throughput clinical data in the context of fundamental biological knowledge. We have extended Corvus, a data warehouse which provides a uniform interface to various forms of Omics data, by providing a SPARQL endpoint. With the querying and reasoning tools made possible by the Semantic Web, we were able to explore quantitative semantic models retrieved from Corvus in the light of systematic biological knowledge. For this paper, we merged semantic models containing genomic, transcriptomic and epigenomic data from melanoma samples with two semantic models of functional data - one containing Gene Ontology (GO) data, the other, regulatory networks constructed from transcription factor binding information. These two semantic models were created in an ad hoc manner but support a common interface for integration with the quantitative semantic models. Such combined semantic models allow us to pose significant translational medicine questions. Here, we study the interplay between a cell's molecular state and its response to anti-cancer therapy by exploring the resistance of cancer cells to Decitabine, a demethylating agent. We were able to generate a testable hypothesis to explain how Decitabine fights cancer - namely, that it targets apoptosis-related gene promoters predominantly in Decitabine-sensitive cell lines, thus conveying its cytotoxic effect by activating the apoptosis pathway. Our research provides a framework whereby similar hypotheses can be developed easily.

An approach for the semantic interoperability of ISO EN 13606 and OpenEHR archetypes.

PubMed

Martínez-Costa, Catalina; Menárguez-Tortosa, Marcos; Fernández-Breis, Jesualdo Tomás

2010-10-01

The communication between health information systems of hospitals and primary care organizations is currently an important challenge to improve the quality of clinical practice and patient safety. However, clinical information is usually distributed among several independent systems that may be syntactically or semantically incompatible. This fact prevents healthcare professionals from accessing clinical information of patients in an understandable and normalized way. In this work, we address the semantic interoperability of two EHR standards: OpenEHR and ISO EN 13606. Both standards follow the dual model approach which distinguishes information and knowledge, this being represented through archetypes. The solution presented here is capable of transforming OpenEHR archetypes into ISO EN 13606 and vice versa by combining Semantic Web and Model-driven Engineering technologies. The resulting software implementation has been tested using publicly available collections of archetypes for both standards.

Development of Semantic Web - Markup Languages, Web Services, Rules, Explanation, Querying, Proof and Reasoning

DTIC Science & Technology

2008-07-01

Study. WWW2006 Workshop on the Models of Trust for the Web (MTW󈧊), Edinburgh, Scotland, May 22, 2006. • Daniel J. Weitzner, Hal Abelson, Tim Berners ...McGuinness gave an invited talk on ontologies in Intel’s Semantic web day. Other invited speakers were Hendler and Berners - Lee . February 4, 2002...Burke (DARPA) concerning ontology tools. July 19-20, 2000. McGuinness met with W3C representatives ( Berners - Lee , Connolly, Lassila) and other

Spatiotemporal-Thematic Data Processing for the Semantic Web

NASA Astrophysics Data System (ADS)

Hakimpour, Farshad; Aleman-Meza, Boanerges; Perry, Matthew; Sheth, Amit

This chapter presents practical approaches to data processing in the space, time and theme dimensions using existing Semantic Web technologies. It describes how we obtain geographic and event data from Internet sources and also how we integrate them into an RDF store. We briefly introduce a set of functionalities in space, time and semantics. These functionalities are implemented based on our existing technology for main-memory-based RDF data processing developed at the LSDIS Lab. A number of these functionalities are exposed as REST Web services. We present two sample client-side applications that are developed using a combination of our services with Google Maps service.

A medical informatics perspective on health informatics 3.0. Findings from the Yearbook 2011 section on health informatics 3.0.

PubMed

Ruch, P

2011-01-01

To summarize current advances of the so-called Web 3.0 and emerging trends of the semantic web. We provide a synopsis of the articles selected for the IMIA Yearbook 2011, from which we attempt to derive a synthetic overview of the today's and future activities in the field. while the state of the research in the field is illustrated by a set of fairly heterogeneous studies, it is possible to identify significant clusters. While the most salient challenge and obsessional target of the semantic web remains its ambition to simply interconnect all available information, it is interesting to observe the developments of complementary research fields such as information sciences and text analytics. The combined expression power and virtually unlimited data aggregation skills of Web 3.0 technologies make it a disruptive instrument to discover new biomedical knowledge. In parallel, such an unprecedented situation creates new threats for patients participating in large-scale genetic studies as Wjst demonstrate how various data set can be coupled to re-identify anonymous genetic information. The best paper selection of articles on decision support shows examples of excellent research on methods concerning original development of core semantic web techniques as well as transdisciplinary achievements as exemplified with literature-based analytics. This selected set of scientific investigations also demonstrates the needs for computerized applications to transform the biomedical data overflow into more operational clinical knowledge with potential threats for confidentiality directly associated with such advances. Altogether these papers support the idea that more elaborated computer tools, likely to combine heterogeneous text and data contents should soon emerge for the benefit of both experimentalists and hopefully clinicians.

A novel adaptive Cuckoo search for optimal query plan generation.

PubMed

Gomathi, Ramalingam; Sharmila, Dhandapani

2014-01-01

The emergence of multiple web pages day by day leads to the development of the semantic web technology. A World Wide Web Consortium (W3C) standard for storing semantic web data is the resource description framework (RDF). To enhance the efficiency in the execution time for querying large RDF graphs, the evolving metaheuristic algorithms become an alternate to the traditional query optimization methods. This paper focuses on the problem of query optimization of semantic web data. An efficient algorithm called adaptive Cuckoo search (ACS) for querying and generating optimal query plan for large RDF graphs is designed in this research. Experiments were conducted on different datasets with varying number of predicates. The experimental results have exposed that the proposed approach has provided significant results in terms of query execution time. The extent to which the algorithm is efficient is tested and the results are documented.

Automated geospatial Web Services composition based on geodata quality requirements

NASA Astrophysics Data System (ADS)

Cruz, Sérgio A. B.; Monteiro, Antonio M. V.; Santos, Rafael

2012-10-01

Service-Oriented Architecture and Web Services technologies improve the performance of activities involved in geospatial analysis with a distributed computing architecture. However, the design of the geospatial analysis process on this platform, by combining component Web Services, presents some open issues. The automated construction of these compositions represents an important research topic. Some approaches to solving this problem are based on AI planning methods coupled with semantic service descriptions. This work presents a new approach using AI planning methods to improve the robustness of the produced geospatial Web Services composition. For this purpose, we use semantic descriptions of geospatial data quality requirements in a rule-based form. These rules allow the semantic annotation of geospatial data and, coupled with the conditional planning method, this approach represents more precisely the situations of nonconformities with geodata quality that may occur during the execution of the Web Service composition. The service compositions produced by this method are more robust, thus improving process reliability when working with a composition of chained geospatial Web Services.

An Ontological Approach to Developing Information Operations Applications for Use on the Semantic Web

DTIC Science & Technology

2008-09-01

IWPC 21 Berners - Lee , Tim . (1999). Weaving the Web. New York: HarperCollins Publishers, Inc. 22... Berners - Lee , Tim . (1999). Weaving the Web. New York: HarperCollins Publishers, Inc. Berners - Lee , T., Hendler, J., & Lassila, O. (2001). The Semantic...environment where software agents roaming from page to page can readily carry out sophisticated tasks for users. T. Berners - Lee , J. Hendler, and O

Semantic-Web Architecture for Electronic Discharge Summary Based on OWL 2.0 Standard.

PubMed

Tahmasebian, Shahram; Langarizadeh, Mostafa; Ghazisaeidi, Marjan; Safdari, Reza

2016-06-01

Patients' electronic medical record contains all information related to treatment processes during hospitalization. One of the most important documents in this record is the record summary. In this document, summary of the whole treatment process is presented which is used for subsequent treatments and other issues pertaining to the treatment. Using suitable architecture for this document, apart from the aforementioned points we can use it in other fields such as data mining or decision making based on the cases. In this study, at first, a model for patient's medical record summary has been suggested using semantic web-based architecture. Then, based on service-oriented architecture and using Java programming language, a software solution was designed and run in a way to generate medical record summary with this structure and at the end, new uses of this structure was explained. in this study a structure for medical record summaries along with corrective points within semantic web has been offered and a software running within Java along with special ontologies are provided. After discussing the project with the experts of medical/health data management and medical informatics as well as clinical experts, it became clear that suggested design for medical record summary apart from covering many issues currently faced in the medical records has also many advantages including its uses in research projects, decision making based on the cases etc.

Enhancing e-Learning Content by Using Semantic Web Technologies

ERIC Educational Resources Information Center

García-González, Herminio; Gayo, José Emilio Labra; del Puerto Paule-Ruiz, María

2017-01-01

We describe a new educational tool that relies on Semantic Web technologies to enhance lessons content. We conducted an experiment with 32 students whose results demonstrate better performance when exposed to our tool in comparison with a plain native tool. Consequently, this prototype opens new possibilities in lessons content enhancement.

Leveraging the Semantic Web for Adaptive Education

ERIC Educational Resources Information Center

Kravcik, Milos; Gasevic, Dragan

2007-01-01

In the area of technology-enhanced learning reusability and interoperability issues essentially influence the productivity and efficiency of learning and authoring solutions. There are two basic approaches how to overcome these problems--one attempts to do it via standards and the other by means of the Semantic Web. In practice, these approaches…

Semantic Web-Driven LMS Architecture towards a Holistic Learning Process Model Focused on Personalization

ERIC Educational Resources Information Center

Kerkiri, Tania

2010-01-01

A comprehensive presentation is here made on the modular architecture of an e-learning platform with a distinctive emphasis on content personalization, combining advantages from semantic web technology, collaborative filtering and recommendation systems. Modules of this architecture handle information about both the domain-specific didactic…

RuleML-Based Learning Object Interoperability on the Semantic Web

ERIC Educational Resources Information Center

Biletskiy, Yevgen; Boley, Harold; Ranganathan, Girish R.

2008-01-01

Purpose: The present paper aims to describe an approach for building the Semantic Web rules for interoperation between heterogeneous learning objects, namely course outlines from different universities, and one of the rule uses: identifying (in)compatibilities between course descriptions. Design/methodology/approach: As proof of concept, a rule…

Hybrid Filtering in Semantic Query Processing

ERIC Educational Resources Information Center

Jeong, Hanjo

2011-01-01

This dissertation presents a hybrid filtering method and a case-based reasoning framework for enhancing the effectiveness of Web search. Web search may not reflect user needs, intent, context, and preferences, because today's keyword-based search is lacking semantic information to capture the user's context and intent in posing the search query.…

A Semantically Enabled Metadata Repository for Solar Irradiance Data Products

NASA Astrophysics Data System (ADS)

Wilson, A.; Cox, M.; Lindholm, D. M.; Nadiadi, I.; Traver, T.

2014-12-01

The Laboratory for Atmospheric and Space Physics, LASP, has been conducting research in Atmospheric and Space science for over 60 years, and providing the associated data products to the public. LASP has a long history, in particular, of making space-based measurements of the solar irradiance, which serves as crucial input to several areas of scientific research, including solar-terrestrial interactions, atmospheric, and climate. LISIRD, the LASP Interactive Solar Irradiance Data Center, serves these datasets to the public, including solar spectral irradiance (SSI) and total solar irradiance (TSI) data. The LASP extended metadata repository, LEMR, is a database of information about the datasets served by LASP, such as parameters, uncertainties, temporal and spectral ranges, current version, alerts, etc. It serves as the definitive, single source of truth for that information. The database is populated with information garnered via web forms and automated processes. Dataset owners keep the information current and verified for datasets under their purview. This information can be pulled dynamically for many purposes. Web sites such as LISIRD can include this information in web page content as it is rendered, ensuring users get current, accurate information. It can also be pulled to create metadata records in various metadata formats, such as SPASE (for heliophysics) and ISO 19115. Once these records are be made available to the appropriate registries, our data will be discoverable by users coming in via those organizations. The database is implemented as a RDF triplestore, a collection of instances of subject-object-predicate data entities identifiable with a URI. This capability coupled with SPARQL over HTTP read access enables semantic queries over the repository contents. To create the repository we leveraged VIVO, an open source semantic web application, to manage and create new ontologies and populate repository content. A variety of ontologies were used in creating the triplestore, including ontologies that came with VIVO such as FOAF. Also, the W3C DCAT ontology was integrated and extended to describe properties of our data products that we needed to capture, such as spectral range. The presentation will describe the architecture, ontology issues, and tools used to create LEMR and plans for its evolution.

Semantic integration of information about orthologs and diseases: the OGO system.

PubMed

Miñarro-Gimenez, Jose Antonio; Egaña Aranguren, Mikel; Martínez Béjar, Rodrigo; Fernández-Breis, Jesualdo Tomás; Madrid, Marisa

2011-12-01

Semantic Web technologies like RDF and OWL are currently applied in life sciences to improve knowledge management by integrating disparate information. Many of the systems that perform such task, however, only offer a SPARQL query interface, which is difficult to use for life scientists. We present the OGO system, which consists of a knowledge base that integrates information of orthologous sequences and genetic diseases, providing an easy to use ontology-constrain driven query interface. Such interface allows the users to define SPARQL queries through a graphical process, therefore not requiring SPARQL expertise. Copyright © 2011 Elsevier Inc. All rights reserved.

Incorporating Web 2.0 Technologies from an Organizational Perspective

NASA Astrophysics Data System (ADS)

Owens, R.

2009-12-01

The Arctic Research Consortium of the United States (ARCUS) provides support for the organization, facilitation, and dissemination of online educational and scientific materials and information to a wide range of stakeholders. ARCUS is currently weaving the fabric of Web 2.0 technologies—web development featuring interactive information sharing and user-centered design—into its structure, both as a tool for information management and for educational outreach. The importance of planning, developing, and maintaining a cohesive online platform in order to integrate data storage and dissemination will be discussed in this presentation, as well as some specific open source technologies and tools currently available, including: ○ Content Management: Any system set up to manage the content of web sites and services. Drupal is a content management system, built in a modular fashion allowing for a powerful set of features including, but not limited to weblogs, forums, event calendars, polling, and more. ○ Faceted Search: Combined with full text indexing, faceted searching allows site visitors to locate information quickly and then provides a set of 'filters' with which to narrow the search results. Apache Solr is a search server with a web-services like API (Application programming interface) that has built in support for faceted searching. ○ Semantic Web: The semantic web refers to the ongoing evolution of the World Wide Web as it begins to incorporate semantic components, which aid in processing requests. OpenCalais is a web service that uses natural language processing, along with other methods, in order to extract meaningful 'tags' from your content. This metadata can then be used to connect people, places, and things throughout your website, enriching the surfing experience for the end user. ○ Web Widgets: A web widget is a portable 'piece of code' that can be embedded easily into web pages by an end user. Timeline is a widget developed as part of the SIMILE project at MIT (Massachusetts Institute of Technology) for displaying time-based events in a clean, horizontal timeline display. Numerous standards, applications, and 3rd party integration services are also available for use in today's Web 2.0 environment. In addition to a cohesive online platform, the following tools can improve networking, information sharing, and increased scientific and educational collaboration: ○ Facebook (Fan pages, social networking, etc) ○ Twitter/Twitterfeed (Automatic updates in 3 steps) ○ Mobify.me (Mobile web) ○ Wimba, Adobe Connect, etc (real time conferencing) Increasingly, the scientific community is being asked to share data and information within and outside disciplines, with K-12 students, and with members of the public and policy-makers. Web 2.0 technologies can easily be set up and utilized to share data and other information to specific audiences in real time, and their simplicity ensures their increasing use by the science community in years to come.

Image processing and applications based on visualizing navigation service

NASA Astrophysics Data System (ADS)

Hwang, Chyi-Wen

2015-07-01

When facing the "overabundant" of semantic web information, in this paper, the researcher proposes the hierarchical classification and visualizing RIA (Rich Internet Application) navigation system: Concept Map (CM) + Semantic Structure (SS) + the Knowledge on Demand (KOD) service. The aim of the Multimedia processing and empirical applications testing, was to investigating the utility and usability of this visualizing navigation strategy in web communication design, into whether it enables the user to retrieve and construct their personal knowledge or not. Furthermore, based on the segment markets theory in the Marketing model, to propose a User Interface (UI) classification strategy and formulate a set of hypermedia design principles for further UI strategy and e-learning resources in semantic web communication. These research findings: (1) Irrespective of whether the simple declarative knowledge or the complex declarative knowledge model is used, the "CM + SS + KOD navigation system" has a better cognition effect than the "Non CM + SS + KOD navigation system". However, for the" No web design experience user", the navigation system does not have an obvious cognition effect. (2) The essential of classification in semantic web communication design: Different groups of user have a diversity of preference needs and different cognitive styles in the CM + SS + KOD navigation system.

WebGIS based on semantic grid model and web services

NASA Astrophysics Data System (ADS)

Zhang, WangFei; Yue, CaiRong; Gao, JianGuo

2009-10-01

As the combination point of the network technology and GIS technology, WebGIS has got the fast development in recent years. With the restriction of Web and the characteristics of GIS, traditional WebGIS has some prominent problems existing in development. For example, it can't accomplish the interoperability of heterogeneous spatial databases; it can't accomplish the data access of cross-platform. With the appearance of Web Service and Grid technology, there appeared great change in field of WebGIS. Web Service provided an interface which can give information of different site the ability of data sharing and inter communication. The goal of Grid technology was to make the internet to a large and super computer, with this computer we can efficiently implement the overall sharing of computing resources, storage resource, data resource, information resource, knowledge resources and experts resources. But to WebGIS, we only implement the physically connection of data and information and these is far from the enough. Because of the different understanding of the world, following different professional regulations, different policies and different habits, the experts in different field will get different end when they observed the same geographic phenomenon and the semantic heterogeneity produced. Since these there are large differences to the same concept in different field. If we use the WebGIS without considering of the semantic heterogeneity, we will answer the questions users proposed wrongly or we can't answer the questions users proposed. To solve this problem, this paper put forward and experienced an effective method of combing semantic grid and Web Services technology to develop WebGIS. In this paper, we studied the method to construct ontology and the method to combine Grid technology and Web Services and with the detailed analysis of computing characteristics and application model in the distribution of data, we designed the WebGIS query system driven by ontology based on Grid technology and Web Services.

Electronic Scientific Data & Literature Aggregation: A Review for Librarians

ERIC Educational Resources Information Center

Losoff, Barbara

2009-01-01

The advent of large-scale digital repositories, along with the need for sharing useful data world-wide, demands change to the current information structure. The merging of digital scientific data with scholarly literature has the potential to fulfill the Semantic Web design principles. This paper will identify factors leading to integration of…

Syntactic and Semantic Specifications in Online English Learners' Dictionaries

ERIC Educational Resources Information Center

Rizo-Rodriguez, Alfonso

2009-01-01

Among the multifarious linguistic resources currently available on the Internet, learners of English as a foreign language, as well as teachers and translators, can effortlessly access a vast variety of electronic dictionaries well suited to a multiplicity of lookup operations. A particular kind of lexicographical work on the Web is the…

Semantic Maps Capturing Organization Knowledge in e-Learning

NASA Astrophysics Data System (ADS)

Mavridis, Androklis; Koumpis, Adamantios; Demetriadis, Stavros N.

e-learning, shows much promise in accessibility and opportunity to learn, due to its asynchronous nature and its ability to transmit knowledge fast and effectively. However without a universal standard for online learning and teaching, many systems are proclaimed as “e-learning-compliant”, offering nothing more than automated services for delivering courses online, providing no additional enhancement to reusability and learner personalization. Hence, the focus is not on providing reusable and learner-centered content, but on developing the technology aspects of e-learning. This current trend has made it crucial to find a more refined definition of what constitutes knowledge in the e-learning context. We propose an e-learning system architecture that makes use of a knowledge model to facilitate continuous dialogue and inquiry-based knowledge learning, by exploiting the full benefits of the semantic web as a medium capable for supplying the web with formalized knowledge.

Applying Semantic Web technologies to improve the retrieval, credibility and use of health-related web resources.

PubMed

Mayer, Miguel A; Karampiperis, Pythagoras; Kukurikos, Antonis; Karkaletsis, Vangelis; Stamatakis, Kostas; Villarroel, Dagmar; Leis, Angela

2011-06-01

The number of health-related websites is increasing day-by-day; however, their quality is variable and difficult to assess. Various "trust marks" and filtering portals have been created in order to assist consumers in retrieving quality medical information. Consumers are using search engines as the main tool to get health information; however, the major problem is that the meaning of the web content is not machine-readable in the sense that computers cannot understand words and sentences as humans can. In addition, trust marks are invisible to search engines, thus limiting their usefulness in practice. During the last five years there have been different attempts to use Semantic Web tools to label health-related web resources to help internet users identify trustworthy resources. This paper discusses how Semantic Web technologies can be applied in practice to generate machine-readable labels and display their content, as well as to empower end-users by providing them with the infrastructure for expressing and sharing their opinions on the quality of health-related web resources.

UBioLab: a web-LABoratory for Ubiquitous in-silico experiments.

PubMed

Bartocci, E; Di Berardini, M R; Merelli, E; Vito, L

2012-03-01

The huge and dynamic amount of bioinformatic resources (e.g., data and tools) available nowadays in Internet represents a big challenge for biologists -for what concerns their management and visualization- and for bioinformaticians -for what concerns the possibility of rapidly creating and executing in-silico experiments involving resources and activities spread over the WWW hyperspace. Any framework aiming at integrating such resources as in a physical laboratory has imperatively to tackle -and possibly to handle in a transparent and uniform way- aspects concerning physical distribution, semantic heterogeneity, co-existence of different computational paradigms and, as a consequence, of different invocation interfaces (i.e., OGSA for Grid nodes, SOAP for Web Services, Java RMI for Java objects, etc.). The framework UBioLab has been just designed and developed as a prototype following the above objective. Several architectural features -as those ones of being fully Web-based and of combining domain ontologies, Semantic Web and workflow techniques- give evidence of an effort in such a direction. The integration of a semantic knowledge management system for distributed (bioinformatic) resources, a semantic-driven graphic environment for defining and monitoring ubiquitous workflows and an intelligent agent-based technology for their distributed execution allows UBioLab to be a semantic guide for bioinformaticians and biologists providing (i) a flexible environment for visualizing, organizing and inferring any (semantics and computational) "type" of domain knowledge (e.g., resources and activities, expressed in a declarative form), (ii) a powerful engine for defining and storing semantic-driven ubiquitous in-silico experiments on the domain hyperspace, as well as (iii) a transparent, automatic and distributed environment for correct experiment executions.

Exploiting Semantic Web Technologies to Develop OWL-Based Clinical Practice Guideline Execution Engines.

PubMed

Jafarpour, Borna; Abidi, Samina Raza; Abidi, Syed Sibte Raza

2016-01-01

Computerizing paper-based CPG and then executing them can provide evidence-informed decision support to physicians at the point of care. Semantic web technologies especially web ontology language (OWL) ontologies have been profusely used to represent computerized CPG. Using semantic web reasoning capabilities to execute OWL-based computerized CPG unties them from a specific custom-built CPG execution engine and increases their shareability as any OWL reasoner and triple store can be utilized for CPG execution. However, existing semantic web reasoning-based CPG execution engines suffer from lack of ability to execute CPG with high levels of expressivity, high cognitive load of computerization of paper-based CPG and updating their computerized versions. In order to address these limitations, we have developed three CPG execution engines based on OWL 1 DL, OWL 2 DL and OWL 2 DL + semantic web rule language (SWRL). OWL 1 DL serves as the base execution engine capable of executing a wide range of CPG constructs, however for executing highly complex CPG the OWL 2 DL and OWL 2 DL + SWRL offer additional executional capabilities. We evaluated the technical performance and medical correctness of our execution engines using a range of CPG. Technical evaluations show the efficiency of our CPG execution engines in terms of CPU time and validity of the generated recommendation in comparison to existing CPG execution engines. Medical evaluations by domain experts show the validity of the CPG-mediated therapy plans in terms of relevance, safety, and ordering for a wide range of patient scenarios.

A semantic web framework to integrate cancer omics data with biological knowledge

PubMed Central

2012-01-01

Background The RDF triple provides a simple linguistic means of describing limitless types of information. Triples can be flexibly combined into a unified data source we call a semantic model. Semantic models open new possibilities for the integration of variegated biological data. We use Semantic Web technology to explicate high throughput clinical data in the context of fundamental biological knowledge. We have extended Corvus, a data warehouse which provides a uniform interface to various forms of Omics data, by providing a SPARQL endpoint. With the querying and reasoning tools made possible by the Semantic Web, we were able to explore quantitative semantic models retrieved from Corvus in the light of systematic biological knowledge. Results For this paper, we merged semantic models containing genomic, transcriptomic and epigenomic data from melanoma samples with two semantic models of functional data - one containing Gene Ontology (GO) data, the other, regulatory networks constructed from transcription factor binding information. These two semantic models were created in an ad hoc manner but support a common interface for integration with the quantitative semantic models. Such combined semantic models allow us to pose significant translational medicine questions. Here, we study the interplay between a cell's molecular state and its response to anti-cancer therapy by exploring the resistance of cancer cells to Decitabine, a demethylating agent. Conclusions We were able to generate a testable hypothesis to explain how Decitabine fights cancer - namely, that it targets apoptosis-related gene promoters predominantly in Decitabine-sensitive cell lines, thus conveying its cytotoxic effect by activating the apoptosis pathway. Our research provides a framework whereby similar hypotheses can be developed easily. PMID:22373303

Leveraging electronic healthcare record standards and semantic web technologies for the identification of patient cohorts

PubMed Central

Fernández-Breis, Jesualdo Tomás; Maldonado, José Alberto; Marcos, Mar; Legaz-García, María del Carmen; Moner, David; Torres-Sospedra, Joaquín; Esteban-Gil, Angel; Martínez-Salvador, Begoña; Robles, Montserrat

2013-01-01

Background The secondary use of electronic healthcare records (EHRs) often requires the identification of patient cohorts. In this context, an important problem is the heterogeneity of clinical data sources, which can be overcome with the combined use of standardized information models, virtual health records, and semantic technologies, since each of them contributes to solving aspects related to the semantic interoperability of EHR data. Objective To develop methods allowing for a direct use of EHR data for the identification of patient cohorts leveraging current EHR standards and semantic web technologies. Materials and methods We propose to take advantage of the best features of working with EHR standards and ontologies. Our proposal is based on our previous results and experience working with both technological infrastructures. Our main principle is to perform each activity at the abstraction level with the most appropriate technology available. This means that part of the processing will be performed using archetypes (ie, data level) and the rest using ontologies (ie, knowledge level). Our approach will start working with EHR data in proprietary format, which will be first normalized and elaborated using EHR standards and then transformed into a semantic representation, which will be exploited by automated reasoning. Results We have applied our approach to protocols for colorectal cancer screening. The results comprise the archetypes, ontologies, and datasets developed for the standardization and semantic analysis of EHR data. Anonymized real data have been used and the patients have been successfully classified by the risk of developing colorectal cancer. Conclusions This work provides new insights in how archetypes and ontologies can be effectively combined for EHR-driven phenotyping. The methodological approach can be applied to other problems provided that suitable archetypes, ontologies, and classification rules can be designed. PMID:23934950

Leveraging electronic healthcare record standards and semantic web technologies for the identification of patient cohorts.

PubMed

Fernández-Breis, Jesualdo Tomás; Maldonado, José Alberto; Marcos, Mar; Legaz-García, María del Carmen; Moner, David; Torres-Sospedra, Joaquín; Esteban-Gil, Angel; Martínez-Salvador, Begoña; Robles, Montserrat

2013-12-01

The secondary use of electronic healthcare records (EHRs) often requires the identification of patient cohorts. In this context, an important problem is the heterogeneity of clinical data sources, which can be overcome with the combined use of standardized information models, virtual health records, and semantic technologies, since each of them contributes to solving aspects related to the semantic interoperability of EHR data. To develop methods allowing for a direct use of EHR data for the identification of patient cohorts leveraging current EHR standards and semantic web technologies. We propose to take advantage of the best features of working with EHR standards and ontologies. Our proposal is based on our previous results and experience working with both technological infrastructures. Our main principle is to perform each activity at the abstraction level with the most appropriate technology available. This means that part of the processing will be performed using archetypes (ie, data level) and the rest using ontologies (ie, knowledge level). Our approach will start working with EHR data in proprietary format, which will be first normalized and elaborated using EHR standards and then transformed into a semantic representation, which will be exploited by automated reasoning. We have applied our approach to protocols for colorectal cancer screening. The results comprise the archetypes, ontologies, and datasets developed for the standardization and semantic analysis of EHR data. Anonymized real data have been used and the patients have been successfully classified by the risk of developing colorectal cancer. This work provides new insights in how archetypes and ontologies can be effectively combined for EHR-driven phenotyping. The methodological approach can be applied to other problems provided that suitable archetypes, ontologies, and classification rules can be designed.

Link Correlated Military Data for Better Decision Support

DTIC Science & Technology

2011-06-01

automatically translated into URI based links, thus can greatly reduce man power cost on software development. 3 Linked Data Technique Tim Berners - Lee ...Linked Data - while Linked Data is usually considered as part of Semantic Web, or “the Semantic Web done right” as described by Tim himself - has been...Required data of automatic link construction mechanism on more kinds of correlations. References [1] B. L. Tim , “The next Web of open, linked data

CelOWS: an ontology based framework for the provision of semantic web services related to biological models.

PubMed

Matos, Ely Edison; Campos, Fernanda; Braga, Regina; Palazzi, Daniele

2010-02-01

The amount of information generated by biological research has lead to an intensive use of models. Mathematical and computational modeling needs accurate description to share, reuse and simulate models as formulated by original authors. In this paper, we introduce the Cell Component Ontology (CelO), expressed in OWL-DL. This ontology captures both the structure of a cell model and the properties of functional components. We use this ontology in a Web project (CelOWS) to describe, query and compose CellML models, using semantic web services. It aims to improve reuse and composition of existent components and allow semantic validation of new models.

Semantic Web Applications and Tools for the Life Sciences: SWAT4LS 2010

PubMed Central

2012-01-01

As Semantic Web technologies mature and new releases of key elements, such as SPARQL 1.1 and OWL 2.0, become available, the Life Sciences continue to push the boundaries of these technologies with ever more sophisticated tools and applications. Unsurprisingly, therefore, interest in the SWAT4LS (Semantic Web Applications and Tools for the Life Sciences) activities have remained high, as was evident during the third international SWAT4LS workshop held in Berlin in December 2010. Contributors to this workshop were invited to submit extended versions of their papers, the best of which are now made available in the special supplement of BMC Bioinformatics. The papers reflect the wide range of work in this area, covering the storage and querying of Life Sciences data in RDF triple stores, tools for the development of biomedical ontologies and the semantics-based integration of Life Sciences as well as clinicial data. PMID:22373274

Semantic Web applications and tools for the life sciences: SWAT4LS 2010.

PubMed

Burger, Albert; Paschke, Adrian; Romano, Paolo; Marshall, M Scott; Splendiani, Andrea

2012-01-25

As Semantic Web technologies mature and new releases of key elements, such as SPARQL 1.1 and OWL 2.0, become available, the Life Sciences continue to push the boundaries of these technologies with ever more sophisticated tools and applications. Unsurprisingly, therefore, interest in the SWAT4LS (Semantic Web Applications and Tools for the Life Sciences) activities have remained high, as was evident during the third international SWAT4LS workshop held in Berlin in December 2010. Contributors to this workshop were invited to submit extended versions of their papers, the best of which are now made available in the special supplement of BMC Bioinformatics. The papers reflect the wide range of work in this area, covering the storage and querying of Life Sciences data in RDF triple stores, tools for the development of biomedical ontologies and the semantics-based integration of Life Sciences as well as clinicial data.

Large scale healthcare data integration and analysis using the semantic web.

PubMed

Timm, John; Renly, Sondra; Farkash, Ariel

2011-01-01

Healthcare data interoperability can only be achieved when the semantics of the content is well defined and consistently implemented across heterogeneous data sources. Achieving these objectives of interoperability requires the collaboration of experts from several domains. This paper describes tooling that integrates Semantic Web technologies with common tools to facilitate cross-domain collaborative development for the purposes of data interoperability. Our approach is divided into stages of data harmonization and representation, model transformation, and instance generation. We applied our approach on Hypergenes, an EU funded project, where we use our method to the Essential Hypertension disease model using a CDA template. Our domain expert partners include clinical providers, clinical domain researchers, healthcare information technology experts, and a variety of clinical data consumers. We show that bringing Semantic Web technologies into the healthcare interoperability toolkit increases opportunities for beneficial collaboration thus improving patient care and clinical research outcomes.

Collaborative E-Learning Using Semantic Course Blog

ERIC Educational Resources Information Center

Lu, Lai-Chen; Yeh, Ching-Long

2008-01-01

Collaborative e-learning delivers many enhancements to e-learning technology; it enables students to collaborate with each other and improves their learning efficiency. Semantic blog combines semantic Web and blog technology that users can import, export, view, navigate, and query the blog. We developed a semantic course blog for collaborative…

Biotea: RDFizing PubMed Central in support for the paper as an interface to the Web of Data

PubMed Central

2013-01-01

Background The World Wide Web has become a dissemination platform for scientific and non-scientific publications. However, most of the information remains locked up in discrete documents that are not always interconnected or machine-readable. The connectivity tissue provided by RDF technology has not yet been widely used to support the generation of self-describing, machine-readable documents. Results In this paper, we present our approach to the generation of self-describing machine-readable scholarly documents. We understand the scientific document as an entry point and interface to the Web of Data. We have semantically processed the full-text, open-access subset of PubMed Central. Our RDF model and resulting dataset make extensive use of existing ontologies and semantic enrichment services. We expose our model, services, prototype, and datasets at http://biotea.idiginfo.org/ Conclusions The semantic processing of biomedical literature presented in this paper embeds documents within the Web of Data and facilitates the execution of concept-based queries against the entire digital library. Our approach delivers a flexible and adaptable set of tools for metadata enrichment and semantic processing of biomedical documents. Our model delivers a semantically rich and highly interconnected dataset with self-describing content so that software can make effective use of it. PMID:23734622

SEE: structured representation of scientific evidence in the biomedical domain using Semantic Web techniques

PubMed Central

2014-01-01

Background Accounts of evidence are vital to evaluate and reproduce scientific findings and integrate data on an informed basis. Currently, such accounts are often inadequate, unstandardized and inaccessible for computational knowledge engineering even though computational technologies, among them those of the semantic web, are ever more employed to represent, disseminate and integrate biomedical data and knowledge. Results We present SEE (Semantic EvidencE), an RDF/OWL based approach for detailed representation of evidence in terms of the argumentative structure of the supporting background for claims even in complex settings. We derive design principles and identify minimal components for the representation of evidence. We specify the Reasoning and Discourse Ontology (RDO), an OWL representation of the model of scientific claims, their subjects, their provenance and their argumentative relations underlying the SEE approach. We demonstrate the application of SEE and illustrate its design patterns in a case study by providing an expressive account of the evidence for certain claims regarding the isolation of the enzyme glutamine synthetase. Conclusions SEE is suited to provide coherent and computationally accessible representations of evidence-related information such as the materials, methods, assumptions, reasoning and information sources used to establish a scientific finding by adopting a consistently claim-based perspective on scientific results and their evidence. SEE allows for extensible evidence representations, in which the level of detail can be adjusted and which can be extended as needed. It supports representation of arbitrary many consecutive layers of interpretation and attribution and different evaluations of the same data. SEE and its underlying model could be a valuable component in a variety of use cases that require careful representation or examination of evidence for data presented on the semantic web or in other formats. PMID:25093070

SEE: structured representation of scientific evidence in the biomedical domain using Semantic Web techniques.

PubMed

Bölling, Christian; Weidlich, Michael; Holzhütter, Hermann-Georg

2014-01-01

Accounts of evidence are vital to evaluate and reproduce scientific findings and integrate data on an informed basis. Currently, such accounts are often inadequate, unstandardized and inaccessible for computational knowledge engineering even though computational technologies, among them those of the semantic web, are ever more employed to represent, disseminate and integrate biomedical data and knowledge. We present SEE (Semantic EvidencE), an RDF/OWL based approach for detailed representation of evidence in terms of the argumentative structure of the supporting background for claims even in complex settings. We derive design principles and identify minimal components for the representation of evidence. We specify the Reasoning and Discourse Ontology (RDO), an OWL representation of the model of scientific claims, their subjects, their provenance and their argumentative relations underlying the SEE approach. We demonstrate the application of SEE and illustrate its design patterns in a case study by providing an expressive account of the evidence for certain claims regarding the isolation of the enzyme glutamine synthetase. SEE is suited to provide coherent and computationally accessible representations of evidence-related information such as the materials, methods, assumptions, reasoning and information sources used to establish a scientific finding by adopting a consistently claim-based perspective on scientific results and their evidence. SEE allows for extensible evidence representations, in which the level of detail can be adjusted and which can be extended as needed. It supports representation of arbitrary many consecutive layers of interpretation and attribution and different evaluations of the same data. SEE and its underlying model could be a valuable component in a variety of use cases that require careful representation or examination of evidence for data presented on the semantic web or in other formats.

Application of Ontologies for Big Earth Data

NASA Astrophysics Data System (ADS)

Huang, T.; Chang, G.; Armstrong, E. M.; Boening, C.

2014-12-01

Connected data is smarter data! Earth Science research infrastructure must do more than just being able to support temporal, geospatial discovery of satellite data. As the Earth Science data archives continue to expand across NASA data centers, the research communities are demanding smarter data services. A successful research infrastructure must be able to present researchers the complete picture, that is, datasets with linked citations, related interdisciplinary data, imageries, current events, social media discussions, and scientific data tools that are relevant to the particular dataset. The popular Semantic Web for Earth and Environmental Terminology (SWEET) ontologies is a collection of ontologies and concepts designed to improve discovery and application of Earth Science data. The SWEET ontologies collection was initially developed to capture the relationships between keywords in the NASA Global Change Master Directory (GCMD). Over the years this popular ontologies collection has expanded to cover over 200 ontologies and 6000 concepts to enable scalable classification of Earth system science concepts and Space science. This presentation discusses the semantic web technologies as the enabling technology for data-intensive science. We will discuss the application of the SWEET ontologies as a critical component in knowledge-driven research infrastructure for some of the recent projects, which include the DARPA Ontological System for Context Artifact and Resources (OSCAR), 2013 NASA ACCESS Virtual Quality Screening Service (VQSS), and the 2013 NASA Sea Level Change Portal (SLCP) projects. The presentation will also discuss the benefits in using semantic web technologies in developing research infrastructure for Big Earth Science Data in an attempt to "accommodate all domains and provide the necessary glue for information to be cross-linked, correlated, and discovered in a semantically rich manner." [1] [1] Savas Parastatidis: A platform for all that we know: creating a knowledge-driven research infrastructure. The Fourth Paradigm 2009: 165-172

Reasoning and Ontologies for Personalized E-Learning in the Semantic Web

ERIC Educational Resources Information Center

Henze, Nicola; Dolog, Peter; Nejdl, Wolfgang

2004-01-01

The challenge of the semantic web is the provision of distributed information with well-defined meaning, understandable for different parties. Particularly, applications should be able to provide individually optimized access to information by taking the individual needs and requirements of the users into account. In this paper we propose a…

71 FR 66315 - Notice of Availability of Invention for Licensing; Government-Owned Invention

Federal Register 2010, 2011, 2012, 2013, 2014

2006-11-14

... Coating and Method of Formulator.//Navy Case No. 97,486: Processing Semantic Markups in Web Ontology... Rotating Clip.//Navy Case No. 97,886: Adding Semantic Support to Existing UDDI Infrastructure.//Navy Case..., Binding, and Integration of Non-Registered Geospatial Web Services.//Navy Case No. 98,094: Novel, Single...

E-Learning System Overview Based on Semantic Web

ERIC Educational Resources Information Center

Alsultanny, Yas A.

2006-01-01

The challenge of the semantic web is the provision of distributed information with well-defined meaning, understandable for different parties. e-Learning is efficient task relevant and just-in-time learning grown from the learning requirements of the new dynamically changing, distributed business world. In this paper we design an e-Learning system…

Science gateways for semantic-web-based life science applications.

PubMed

Ardizzone, Valeria; Bruno, Riccardo; Calanducci, Antonio; Carrubba, Carla; Fargetta, Marco; Ingrà, Elisa; Inserra, Giuseppina; La Rocca, Giuseppe; Monforte, Salvatore; Pistagna, Fabrizio; Ricceri, Rita; Rotondo, Riccardo; Scardaci, Diego; Barbera, Roberto

2012-01-01

In this paper we present the architecture of a framework for building Science Gateways supporting official standards both for user authentication and authorization and for middleware-independent job and data management. Two use cases of the customization of the Science Gateway framework for Semantic-Web-based life science applications are also described.

Efficient Results in Semantic Interoperability for Health Care. Findings from the Section on Knowledge Representation and Management.

PubMed

Soualmia, L F; Charlet, J

2016-11-10

To summarize excellent current research in the field of Knowledge Representation and Management (KRM) within the health and medical care domain. We provide a synopsis of the 2016 IMIA selected articles as well as a related synthetic overview of the current and future field activities. A first step of the selection was performed through MEDLINE querying with a list of MeSH descriptors completed by a list of terms adapted to the KRM section. The second step of the selection was completed by the two section editors who separately evaluated the set of 1,432 articles. The third step of the selection consisted of a collective work that merged the evaluation results to retain 15 articles for peer-review. The selection and evaluation process of this Yearbook's section on Knowledge Representation and Management has yielded four excellent and interesting articles regarding semantic interoperability for health care by gathering heterogeneous sources (knowledge and data) and auditing ontologies. In the first article, the authors present a solution based on standards and Semantic Web technologies to access distributed and heterogeneous datasets in the domain of breast cancer clinical trials. The second article describes a knowledge-based recommendation system that relies on ontologies and Semantic Web rules in the context of chronic diseases dietary. The third article is related to concept-recognition and text-mining to derive common human diseases model and a phenotypic network of common diseases. In the fourth article, the authors highlight the need for auditing the SNOMED CT. They propose to use a crowdbased method for ontology engineering. The current research activities further illustrate the continuous convergence of Knowledge Representation and Medical Informatics, with a focus this year on dedicated tools and methods to advance clinical care by proposing solutions to cope with the problem of semantic interoperability. Indeed, there is a need for powerful tools able to manage and interpret complex, large-scale and distributed datasets and knowledge bases, but also a need for user-friendly tools developed for the clinicians in their daily practice.

Entrez Neuron RDFa: a pragmatic semantic web application for data integration in neuroscience research.

PubMed

Samwald, Matthias; Lim, Ernest; Masiar, Peter; Marenco, Luis; Chen, Huajun; Morse, Thomas; Mutalik, Pradeep; Shepherd, Gordon; Miller, Perry; Cheung, Kei-Hoi

2009-01-01

The amount of biomedical data available in Semantic Web formats has been rapidly growing in recent years. While these formats are machine-friendly, user-friendly web interfaces allowing easy querying of these data are typically lacking. We present "Entrez Neuron", a pilot neuron-centric interface that allows for keyword-based queries against a coherent repository of OWL ontologies. These ontologies describe neuronal structures, physiology, mathematical models and microscopy images. The returned query results are organized hierarchically according to brain architecture. Where possible, the application makes use of entities from the Open Biomedical Ontologies (OBO) and the 'HCLS knowledgebase' developed by the W3C Interest Group for Health Care and Life Science. It makes use of the emerging RDFa standard to embed ontology fragments and semantic annotations within its HTML-based user interface. The application and underlying ontologies demonstrate how Semantic Web technologies can be used for information integration within a curated information repository and between curated information repositories. It also demonstrates how information integration can be accomplished on the client side, through simple copying and pasting of portions of documents that contain RDFa markup.

An introduction to the Semantic Web for health sciences librarians.

PubMed

Robu, Ioana; Robu, Valentin; Thirion, Benoit

2006-04-01

The paper (1) introduces health sciences librarians to the main concepts and principles of the Semantic Web (SW) and (2) briefly reviews a number of projects on the handling of biomedical information that uses SW technology. The paper is structured into two main parts. "Semantic Web Technology" provides a high-level description, with examples, of the main standards and concepts: extensible markup language (XML), Resource Description Framework (RDF), RDF Schema (RDFS), ontologies, and their utility in information retrieval, concluding with mention of more advanced SW languages and their characteristics. "Semantic Web Applications and Research Projects in the Biomedical Field" is a brief review of the Unified Medical Language System (UMLS), Generalised Architecture for Languages, Encyclopedias and Nomenclatures in Medicine (GALEN), HealthCyberMap, LinkBase, and the thesaurus of the National Cancer Institute (NCI). The paper also mentions other benefits and by-products of the SW, citing projects related to them. Some of the problems facing the SW vision are presented, especially the ways in which the librarians' expertise in organizing knowledge and in structuring information may contribute to SW projects.

Component Models for Semantic Web Languages

NASA Astrophysics Data System (ADS)

Henriksson, Jakob; Aßmann, Uwe

Intelligent applications and agents on the Semantic Web typically need to be specified with, or interact with specifications written in, many different kinds of formal languages. Such languages include ontology languages, data and metadata query languages, as well as transformation languages. As learnt from years of experience in development of complex software systems, languages need to support some form of component-based development. Components enable higher software quality, better understanding and reusability of already developed artifacts. Any component approach contains an underlying component model, a description detailing what valid components are and how components can interact. With the multitude of languages developed for the Semantic Web, what are their underlying component models? Do we need to develop one for each language, or is a more general and reusable approach achievable? We present a language-driven component model specification approach. This means that a component model can be (automatically) generated from a given base language (actually, its specification, e.g. its grammar). As a consequence, we can provide components for different languages and simplify the development of software artifacts used on the Semantic Web.

The EMBRACE web service collection

PubMed Central

Pettifer, Steve; Ison, Jon; Kalaš, Matúš; Thorne, Dave; McDermott, Philip; Jonassen, Inge; Liaquat, Ali; Fernández, José M.; Rodriguez, Jose M.; Partners, INB-; Pisano, David G.; Blanchet, Christophe; Uludag, Mahmut; Rice, Peter; Bartaseviciute, Edita; Rapacki, Kristoffer; Hekkelman, Maarten; Sand, Olivier; Stockinger, Heinz; Clegg, Andrew B.; Bongcam-Rudloff, Erik; Salzemann, Jean; Breton, Vincent; Attwood, Teresa K.; Cameron, Graham; Vriend, Gert

2010-01-01

The EMBRACE (European Model for Bioinformatics Research and Community Education) web service collection is the culmination of a 5-year project that set out to investigate issues involved in developing and deploying web services for use in the life sciences. The project concluded that in order for web services to achieve widespread adoption, standards must be defined for the choice of web service technology, for semantically annotating both service function and the data exchanged, and a mechanism for discovering services must be provided. Building on this, the project developed: EDAM, an ontology for describing life science web services; BioXSD, a schema for exchanging data between services; and a centralized registry (http://www.embraceregistry.net) that collects together around 1000 services developed by the consortium partners. This article presents the current status of the collection and its associated recommendations and standards definitions. PMID:20462862

Semantic similarity measures in the biomedical domain by leveraging a web search engine.

PubMed

Hsieh, Sheau-Ling; Chang, Wen-Yung; Chen, Chi-Huang; Weng, Yung-Ching

2013-07-01

Various researches in web related semantic similarity measures have been deployed. However, measuring semantic similarity between two terms remains a challenging task. The traditional ontology-based methodologies have a limitation that both concepts must be resided in the same ontology tree(s). Unfortunately, in practice, the assumption is not always applicable. On the other hand, if the corpus is sufficiently adequate, the corpus-based methodologies can overcome the limitation. Now, the web is a continuous and enormous growth corpus. Therefore, a method of estimating semantic similarity is proposed via exploiting the page counts of two biomedical concepts returned by Google AJAX web search engine. The features are extracted as the co-occurrence patterns of two given terms P and Q, by querying P, Q, as well as P AND Q, and the web search hit counts of the defined lexico-syntactic patterns. These similarity scores of different patterns are evaluated, by adapting support vector machines for classification, to leverage the robustness of semantic similarity measures. Experimental results validating against two datasets: dataset 1 provided by A. Hliaoutakis; dataset 2 provided by T. Pedersen, are presented and discussed. In dataset 1, the proposed approach achieves the best correlation coefficient (0.802) under SNOMED-CT. In dataset 2, the proposed method obtains the best correlation coefficient (SNOMED-CT: 0.705; MeSH: 0.723) with physician scores comparing with measures of other methods. However, the correlation coefficients (SNOMED-CT: 0.496; MeSH: 0.539) with coder scores received opposite outcomes. In conclusion, the semantic similarity findings of the proposed method are close to those of physicians' ratings. Furthermore, the study provides a cornerstone investigation for extracting fully relevant information from digitizing, free-text medical records in the National Taiwan University Hospital database.

SIDD: A Semantically Integrated Database towards a Global View of Human Disease

PubMed Central

Cheng, Liang; Wang, Guohua; Li, Jie; Zhang, Tianjiao; Xu, Peigang; Wang, Yadong

2013-01-01

Background A number of databases have been developed to collect disease-related molecular, phenotypic and environmental features (DR-MPEs), such as genes, non-coding RNAs, genetic variations, drugs, phenotypes and environmental factors. However, each of current databases focused on only one or two DR-MPEs. There is an urgent demand to develop an integrated database, which can establish semantic associations among disease-related databases and link them to provide a global view of human disease at the biological level. This database, once developed, will facilitate researchers to query various DR-MPEs through disease, and investigate disease mechanisms from different types of data. Methodology To establish an integrated disease-associated database, disease vocabularies used in different databases are mapped to Disease Ontology (DO) through semantic match. 4,284 and 4,186 disease terms from Medical Subject Headings (MeSH) and Online Mendelian Inheritance in Man (OMIM) respectively are mapped to DO. Then, the relationships between DR-MPEs and diseases are extracted and merged from different source databases for reducing the data redundancy. Conclusions A semantically integrated disease-associated database (SIDD) is developed, which integrates 18 disease-associated databases, for researchers to browse multiple types of DR-MPEs in a view. A web interface allows easy navigation for querying information through browsing a disease ontology tree or searching a disease term. Furthermore, a network visualization tool using Cytoscape Web plugin has been implemented in SIDD. It enhances the SIDD usage when viewing the relationships between diseases and DR-MPEs. The current version of SIDD (Jul 2013) documents 4,465,131 entries relating to 139,365 DR-MPEs, and to 3,824 human diseases. The database can be freely accessed from: http://mlg.hit.edu.cn/SIDD. PMID:24146757

Software analysis in the semantic web

NASA Astrophysics Data System (ADS)

Taylor, Joshua; Hall, Robert T.

2013-05-01

Many approaches in software analysis, particularly dynamic malware analyis, benefit greatly from the use of linked data and other Semantic Web technology. In this paper, we describe AIS, Inc.'s Semantic Extractor (SemEx) component from the Malware Analysis and Attribution through Genetic Information (MAAGI) effort, funded under DARPA's Cyber Genome program. The SemEx generates OWL-based semantic models of high and low level behaviors in malware samples from system call traces generated by AIS's introspective hypervisor, IntroVirtTM. Within MAAGI, these semantic models were used by modules that cluster malware samples by functionality, and construct "genealogical" malware lineages. Herein, we describe the design, implementation, and use of the SemEx, as well as the C2DB, an OWL ontology used for representing software behavior and cyber-environments.

A Learning Content Authoring Approach Based on Semantic Technologies and Social Networking: An Empirical Study

ERIC Educational Resources Information Center

Nesic, Sasa; Gasevic, Dragan; Jazayeri, Mehdi; Landoni, Monica

2011-01-01

Semantic web technologies have been applied to many aspects of learning content authoring including semantic annotation, semantic search, dynamic assembly, and personalization of learning content. At the same time, social networking services have started to play an important role in the authoring process by supporting authors' collaborative…

Advantages of Thesaurus Representation Using the Simple Knowledge Organization System (SKOS) Compared with Proposed Alternatives

ERIC Educational Resources Information Center

Pastor-Sanchez, Juan-Antonio; Martinez Mendez, Francisco Javier; Rodriguez-Munoz, Jose Vicente

2009-01-01

Introduction: This paper presents an analysis of the Simple Knowledge Organization System (SKOS) compared with other alternatives for thesaurus representation in the Semantic Web. Method: Based on functional and structural changes of thesauri, provides an overview of the current context in which lexical paradigm is abandoned in favour of the…

UBioLab: a web-laboratory for ubiquitous in-silico experiments.

PubMed

Bartocci, Ezio; Cacciagrano, Diletta; Di Berardini, Maria Rita; Merelli, Emanuela; Vito, Leonardo

2012-07-09

The huge and dynamic amount of bioinformatic resources (e.g., data and tools) available nowadays in Internet represents a big challenge for biologists –for what concerns their management and visualization– and for bioinformaticians –for what concerns the possibility of rapidly creating and executing in-silico experiments involving resources and activities spread over the WWW hyperspace. Any framework aiming at integrating such resources as in a physical laboratory has imperatively to tackle –and possibly to handle in a transparent and uniform way– aspects concerning physical distribution, semantic heterogeneity, co-existence of different computational paradigms and, as a consequence, of different invocation interfaces (i.e., OGSA for Grid nodes, SOAP for Web Services, Java RMI for Java objects, etc.). The framework UBioLab has been just designed and developed as a prototype following the above objective. Several architectural features –as those ones of being fully Web-based and of combining domain ontologies, Semantic Web and workflow techniques– give evidence of an effort in such a direction. The integration of a semantic knowledge management system for distributed (bioinformatic) resources, a semantic-driven graphic environment for defining and monitoring ubiquitous workflows and an intelligent agent-based technology for their distributed execution allows UBioLab to be a semantic guide for bioinformaticians and biologists providing (i) a flexible environment for visualizing, organizing and inferring any (semantics and computational) "type" of domain knowledge (e.g., resources and activities, expressed in a declarative form), (ii) a powerful engine for defining and storing semantic-driven ubiquitous in-silico experiments on the domain hyperspace, as well as (iii) a transparent, automatic and distributed environment for correct experiment executions.

Design and Applications of a GeoSemantic Framework for Integration of Data and Model Resources in Hydrologic Systems

NASA Astrophysics Data System (ADS)

Elag, M.; Kumar, P.

2016-12-01

Hydrologists today have to integrate resources such as data and models, which originate and reside in multiple autonomous and heterogeneous repositories over the Web. Several resource management systems have emerged within geoscience communities for sharing long-tail data, which are collected by individual or small research groups, and long-tail models, which are developed by scientists or small modeling communities. While these systems have increased the availability of resources within geoscience domains, deficiencies remain due to the heterogeneity in the methods, which are used to describe, encode, and publish information about resources over the Web. This heterogeneity limits our ability to access the right information in the right context so that it can be efficiently retrieved and understood without the Hydrologist's mediation. A primary challenge of the Web today is the lack of the semantic interoperability among the massive number of resources, which already exist and are continually being generated at rapid rates. To address this challenge, we have developed a decentralized GeoSemantic (GS) framework, which provides three sets of micro-web services to support (i) semantic annotation of resources, (ii) semantic alignment between the metadata of two resources, and (iii) semantic mediation among Standard Names. Here we present the design of the framework and demonstrate its application for semantic integration between data and models used in the IML-CZO. First we show how the IML-CZO data are annotated using the Semantic Annotation Services. Then we illustrate how the Resource Alignment Services and Knowledge Integration Services are used to create a semantic workflow among TopoFlow model, which is a spatially-distributed hydrologic model and the annotated data. Results of this work are (i) a demonstration of how the GS framework advances the integration of heterogeneous data and models of water-related disciplines by seamless handling of their semantic heterogeneity, (ii) an introduction of new paradigm for reusing existing and new standards as well as tools and models without the need of their implementation in the Cyberinfrastructures of water-related disciplines, and (iii) an investigation of a methodology by which distributed models can be coupled in a workflow using the GS services.

An ontology-driven tool for structured data acquisition using Web forms.

PubMed

Gonçalves, Rafael S; Tu, Samson W; Nyulas, Csongor I; Tierney, Michael J; Musen, Mark A

2017-08-01

Structured data acquisition is a common task that is widely performed in biomedicine. However, current solutions for this task are far from providing a means to structure data in such a way that it can be automatically employed in decision making (e.g., in our example application domain of clinical functional assessment, for determining eligibility for disability benefits) based on conclusions derived from acquired data (e.g., assessment of impaired motor function). To use data in these settings, we need it structured in a way that can be exploited by automated reasoning systems, for instance, in the Web Ontology Language (OWL); the de facto ontology language for the Web. We tackle the problem of generating Web-based assessment forms from OWL ontologies, and aggregating input gathered through these forms as an ontology of "semantically-enriched" form data that can be queried using an RDF query language, such as SPARQL. We developed an ontology-based structured data acquisition system, which we present through its specific application to the clinical functional assessment domain. We found that data gathered through our system is highly amenable to automatic analysis using queries. We demonstrated how ontologies can be used to help structuring Web-based forms and to semantically enrich the data elements of the acquired structured data. The ontologies associated with the enriched data elements enable automated inferences and provide a rich vocabulary for performing queries.

On2broker: Semantic-Based Access to Information Sources at the WWW.

ERIC Educational Resources Information Center

Fensel, Dieter; Angele, Jurgen; Decker, Stefan; Erdmann, Michael; Schnurr, Hans-Peter; Staab, Steffen; Studer, Rudi; Witt, Andreas

On2broker provides brokering services to improve access to heterogeneous, distributed, and semistructured information sources as they are presented in the World Wide Web. It relies on the use of ontologies to make explicit the semantics of Web pages. This paper discusses the general architecture and main components (i.e., query engine, information…

Case-Based Learning, Pedagogical Innovation, and Semantic Web Technologies

ERIC Educational Resources Information Center

Martinez-Garcia, A.; Morris, S.; Tscholl, M.; Tracy, F.; Carmichael, P.

2012-01-01

This paper explores the potential of Semantic Web technologies to support teaching and learning in a variety of higher education settings in which some form of case-based learning is the pedagogy of choice. It draws on the empirical work of a major three year research and development project in the United Kingdom: "Ensemble: Semantic…

What Can the Semantic Web Do for Adaptive Educational Hypermedia?

ERIC Educational Resources Information Center

Cristea, Alexandra I.

2004-01-01

Semantic Web and Adaptive Hypermedia come from different backgrounds, but it turns out that actually, they can benefit from each other, and that their confluence can lead to synergistic effects. This encounter can influence several fields, among which an important one is Education. This paper presents an analysis of this encounter, first from a…

Games and Simulations in Online Learning: Research and Development Frameworks

ERIC Educational Resources Information Center

Gibson, David; Aldrich, Clark; Prensky, Marc

2007-01-01

Games and Simulations in Online Learning: Research and Development Frameworks examines the potential of games and simulations in online learning, and how the future could look as developers learn to use the emerging capabilities of the Semantic Web. It presents a general understanding of how the Semantic Web will impact education and how games and…

The Virtual Solar-Terrestrial Observatory; access to and use of diverse solar and solar- terrestrial data.

NASA Astrophysics Data System (ADS)

Fox, P.; McGuinness, D.; Cinquini, L.; West, P.; Garcia, J.; Zednik, S.; Benedict, J.

2008-05-01

This presentation will demonstrate how users and other data providers can utilize the Virtual Solar-Terrestrial Observatory (VSTO) to find, access and use diverse data holdings from the disciplines of solar, solar-terrestrial and space physics. VSTO provides a web portal, web services and a native applications programming interface for various levels of users. Since these access methods are based on semantic web technologies and refer to the VSTO ontology, users also have the option of taking advantage of value added services when accessing and using the data. We present example of both conventional use of VSTO as well as the advanced semantics use. Finally, we present our future directions for VSTO and semantic data frameworks in general.

The Virtual Solar-Terrestrial Observatory; access to and use of diverse solar and solar-terrestrial data

NASA Astrophysics Data System (ADS)

Fox, P.

2007-05-01

This presentation will demonstrate how users and other data providers can utilize the Virtual Solar-Terrestrial Observatory (VSTO) to find, access and use diverse data holdings from the disciplines of solar, solar-terrestrial and space physics. VSTO provides a web portal, web services and a native applications programming interface for various levels of users. Since these access methods are based on semantic web technologies and refer to the VSTO ontology, users also have the option of taking advantage of value added services when accessing and using the data. We present example of both conventional use of VSTO as well as the advanced semantics use. Finally, we present our future directions for VSTO and semantic data frameworks in general.

Enhanced reproducibility of SADI web service workflows with Galaxy and Docker.

PubMed

Aranguren, Mikel Egaña; Wilkinson, Mark D

2015-01-01

Semantic Web technologies have been widely applied in the life sciences, for example by data providers such as OpenLifeData and through web services frameworks such as SADI. The recently reported OpenLifeData2SADI project offers access to the vast OpenLifeData data store through SADI services. This article describes how to merge data retrieved from OpenLifeData2SADI with other SADI services using the Galaxy bioinformatics analysis platform, thus making this semantic data more amenable to complex analyses. This is demonstrated using a working example, which is made distributable and reproducible through a Docker image that includes SADI tools, along with the data and workflows that constitute the demonstration. The combination of Galaxy and Docker offers a solution for faithfully reproducing and sharing complex data retrieval and analysis workflows based on the SADI Semantic web service design patterns.

Facilitating NCAR Data Discovery by Connecting Related Resources

NASA Astrophysics Data System (ADS)

Rosati, A.

2012-12-01

Linking datasets, creators, and users by employing the proper standards helps to increase the impact of funded research. In order for users to find a dataset, it must first be named. Data citations play the important role of giving datasets a persistent presence by assigning a formal "name" and location. This project focuses on the next step of the "name-find-use" sequence: enhancing discoverability of NCAR data by connecting related resources on the web. By examining metadata schemas that document datasets, I examined how Semantic Web approaches can help to ensure the widest possible range of data users. The focus was to move from search engine optimization (SEO) to information connectivity. Two main markup types are very visible in the Semantic Web and applicable to scientific dataset discovery: The Open Archives Initiative-Object Reuse and Exchange (OAI-ORE - www.openarchives.org) and Microdata (HTML5 and www.schema.org). My project creates pilot aggregations of related resources using both markup types for three case studies: The North American Regional Climate Change Assessment Program (NARCCAP) dataset and related publications, the Palmer Drought Severity Index (PSDI) animation and image files from NCAR's Visualization Lab (VisLab), and the multidisciplinary data types and formats from the Advanced Cooperative Arctic Data and Information Service (ACADIS). This project documents the differences between these markups and how each creates connectedness on the web. My recommendations point toward the most efficient and effective markup schema for aggregating resources within the three case studies based on the following assessment criteria: ease of use, current state of support and adoption of technology, integration with typical web tools, available vocabularies and geoinformatic standards, interoperability with current repositories and access portals (e.g. ESG, Java), and relation to data citation tools and methods.

Connecting geoscience systems and data using Linked Open Data in the Web of Data

NASA Astrophysics Data System (ADS)

Ritschel, Bernd; Neher, Günther; Iyemori, Toshihiko; Koyama, Yukinobu; Yatagai, Akiyo; Murayama, Yasuhiro; Galkin, Ivan; King, Todd; Fung, Shing F.; Hughes, Steve; Habermann, Ted; Hapgood, Mike; Belehaki, Anna

2014-05-01

Linked Data or Linked Open Data (LOD) in the realm of free and publically accessible data is one of the most promising and most used semantic Web frameworks connecting various types of data and vocabularies including geoscience and related domains. The semantic Web extension to the commonly existing and used World Wide Web is based on the meaning of entities and relationships or in different words classes and properties used for data in a global data and information space, the Web of Data. LOD data is referenced and mash-uped by URIs and is retrievable using simple parameter controlled HTTP-requests leading to a result which is human-understandable or machine-readable. Furthermore the publishing and mash-up of data in the semantic Web realm is realized by specific Web standards, such as RDF, RDFS, OWL and SPARQL defined for the Web of Data. Semantic Web based mash-up is the Web method to aggregate and reuse various contents from different sources, such as e.g. using FOAF as a model and vocabulary for the description of persons and organizations -in our case- related to geoscience projects, instruments, observations, data and so on. On the example of three different geoscience data and information management systems, such as ESPAS, IUGONET and GFZ ISDC and the associated science data and related metadata or better called context data, the concept of the mash-up of systems and data using the semantic Web approach and the Linked Open Data framework is described in this publication. Because the three systems are based on different data models, data storage structures and technical implementations an extra semantic Web layer upon the existing interfaces is used for mash-up solutions. In order to satisfy the semantic Web standards, data transition processes, such as the transfer of content stored in relational databases or mapped in XML documents into SPARQL capable databases or endpoints using D2R or XSLT is necessary. In addition, the use of mapped and/or merged domain specific and cross-domain vocabularies in the sense of terminological ontologies are the foundation for a virtually unified data retrieval and access in IUGONET, ESPAS and GFZ ISDC data management systems. SPARQL endpoints realized either by originally RDF databases, e.g. Virtuoso or by virtual SPARQL endpoints, e.g. D2R services enable an only upon Web standard-based mash-up of domain-specific systems and data, such as in this case the space weather and geomagnetic domain but also cross-domain connection to data and vocabularies, e.g. related to NASA's VxOs, particularly VWO or NASA's PDS data system within LOD. LOD - Linked Open Data RDF - Resource Description Framework RDFS - RDF Schema OWL - Ontology Web Language SPARQL - SPARQL Protocol and RDF Query Language FOAF - Friends of a Friend ontology ESPAS - Near Earth Space Data Infrastructure for e-Science (Project) IUGONET - Inter-university Upper Atmosphere Global Observation Network (Project) GFZ ISDC - German Research Centre for Geosciences Information System and Data Center XML - Extensible Mark-up Language D2R - (Relational) Database to RDF (Transformation) XSLT - Extensible Stylesheet Language Transformation Virtuoso - OpenLink Virtuoso Universal Server (including RDF data management) NASA - National Aeronautics and Space Administration VOx - Virtual Observatories VWO - Virtual Wave Observatory PDS - Planetary Data System

An Automated Data Fusion Process for an Air Defense Scenario

DTIC Science & Technology

2011-06-01

and Applications, Proceedings of the IEEE, 77(4)541-580, April of 1989. [4] – Antoniou, G. e Harmelen, F.V. A Semantic Web Primer-Second Edition. The...Instituto Tecnológico de Aeronáutica, São Jose dos Campos, SP, Brazil, 2004. [10] – “What is a Web Service?”, at January, 20, 2011, from http://www.w3...org/TR/ws- arch/#introduction [11] – Yasmine Charif, “An Overview of Semantic Web Services Composition Approaches”, Eletronic Notes in Theorical

Semantic-JSON: a lightweight web service interface for Semantic Web contents integrating multiple life science databases.

PubMed

Kobayashi, Norio; Ishii, Manabu; Takahashi, Satoshi; Mochizuki, Yoshiki; Matsushima, Akihiro; Toyoda, Tetsuro

2011-07-01

Global cloud frameworks for bioinformatics research databases become huge and heterogeneous; solutions face various diametric challenges comprising cross-integration, retrieval, security and openness. To address this, as of March 2011 organizations including RIKEN published 192 mammalian, plant and protein life sciences databases having 8.2 million data records, integrated as Linked Open or Private Data (LOD/LPD) using SciNetS.org, the Scientists' Networking System. The huge quantity of linked data this database integration framework covers is based on the Semantic Web, where researchers collaborate by managing metadata across public and private databases in a secured data space. This outstripped the data query capacity of existing interface tools like SPARQL. Actual research also requires specialized tools for data analysis using raw original data. To solve these challenges, in December 2009 we developed the lightweight Semantic-JSON interface to access each fragment of linked and raw life sciences data securely under the control of programming languages popularly used by bioinformaticians such as Perl and Ruby. Researchers successfully used the interface across 28 million semantic relationships for biological applications including genome design, sequence processing, inference over phenotype databases, full-text search indexing and human-readable contents like ontology and LOD tree viewers. Semantic-JSON services of SciNetS.org are provided at http://semanticjson.org.

PIDs, Types and the Semantic Web

NASA Astrophysics Data System (ADS)

Schwardmann, Ulrich

2017-04-01

PID Information Types are becoming a crucial role in scientific data management because they can provide state (what) and binding (where) information about digital objects as attributes of the PID. This is a similar but much more flexible approach than the well known mime type characterization, because both of these types concepts allow to decide about preconditions for processes in advance and before touching the data. One aspect of this is the need for standards and correctness of the used types to ensure reliability for the processes operating on the digital objects. This requires registries and schemas for PID InfoTypes and suggests an automated schema generation process. Such a process in combination with data type registries will be described in more detail in the intended talk. Another aspect of PID InfoTypes is its intrinsic grammar as subject-predicate-object triple, with the PID as subject, the type as predicate and its value (often again a PID) as object in this relation. Given the registration of types and the proposed syntactical rigidness of the value, guaranteed by the schema, together with the use of PIDs in subject and predicate, the type concept has the ability to overcome the fuzziness and lack of reliability of semantic web categories with its URL references and possibly changing locations and content. The intended talk will also describe this approach in more detail, discusses the differences to linked data and describes some necessary technological developments for the type concept to keep up with the possibilities currently provided by the semantic web.

Formalization of treatment guidelines using Fuzzy Cognitive Maps and semantic web tools.

PubMed

Papageorgiou, Elpiniki I; Roo, Jos De; Huszka, Csaba; Colaert, Dirk

2012-02-01

Therapy decision making and support in medicine deals with uncertainty and needs to take into account the patient's clinical parameters, the context of illness and the medical knowledge of the physician and guidelines to recommend a treatment therapy. This research study is focused on the formalization of medical knowledge using a cognitive process, called Fuzzy Cognitive Maps (FCMs) and semantic web approach. The FCM technique is capable of dealing with situations including uncertain descriptions using similar procedure such as human reasoning does. Thus, it was selected for the case of modeling and knowledge integration of clinical practice guidelines. The semantic web tools were established to implement the FCM approach. The knowledge base was constructed from the clinical guidelines as the form of if-then fuzzy rules. These fuzzy rules were transferred to FCM modeling technique and, through the semantic web tools, the whole formalization was accomplished. The problem of urinary tract infection (UTI) in adult community was examined for the proposed approach. Forty-seven clinical concepts and eight therapy concepts were identified for the antibiotic treatment therapy problem of UTIs. A preliminary pilot-evaluation study with 55 patient cases showed interesting findings; 91% of the antibiotic treatments proposed by the implemented approach were in fully agreement with the guidelines and physicians' opinions. The results have shown that the suggested approach formalizes medical knowledge efficiently and gives a front-end decision on antibiotics' suggestion for cystitis. Concluding, modeling medical knowledge/therapeutic guidelines using cognitive methods and web semantic tools is both reliable and useful. Copyright © 2011 Elsevier Inc. All rights reserved.

Construction of an ortholog database using the semantic web technology for integrative analysis of genomic data.

PubMed

Chiba, Hirokazu; Nishide, Hiroyo; Uchiyama, Ikuo

2015-01-01

Recently, various types of biological data, including genomic sequences, have been rapidly accumulating. To discover biological knowledge from such growing heterogeneous data, a flexible framework for data integration is necessary. Ortholog information is a central resource for interlinking corresponding genes among different organisms, and the Semantic Web provides a key technology for the flexible integration of heterogeneous data. We have constructed an ortholog database using the Semantic Web technology, aiming at the integration of numerous genomic data and various types of biological information. To formalize the structure of the ortholog information in the Semantic Web, we have constructed the Ortholog Ontology (OrthO). While the OrthO is a compact ontology for general use, it is designed to be extended to the description of database-specific concepts. On the basis of OrthO, we described the ortholog information from our Microbial Genome Database for Comparative Analysis (MBGD) in the form of Resource Description Framework (RDF) and made it available through the SPARQL endpoint, which accepts arbitrary queries specified by users. In this framework based on the OrthO, the biological data of different organisms can be integrated using the ortholog information as a hub. Besides, the ortholog information from different data sources can be compared with each other using the OrthO as a shared ontology. Here we show some examples demonstrating that the ortholog information described in RDF can be used to link various biological data such as taxonomy information and Gene Ontology. Thus, the ortholog database using the Semantic Web technology can contribute to biological knowledge discovery through integrative data analysis.

Exploiting semantic linkages among multiple sources for semantic information retrieval

NASA Astrophysics Data System (ADS)

Li, JianQiang; Yang, Ji-Jiang; Liu, Chunchen; Zhao, Yu; Liu, Bo; Shi, Yuliang

2014-07-01

The vision of the Semantic Web is to build a global Web of machine-readable data to be consumed by intelligent applications. As the first step to make this vision come true, the initiative of linked open data has fostered many novel applications aimed at improving data accessibility in the public Web. Comparably, the enterprise environment is so different from the public Web that most potentially usable business information originates in an unstructured form (typically in free text), which poses a challenge for the adoption of semantic technologies in the enterprise environment. Considering that the business information in a company is highly specific and centred around a set of commonly used concepts, this paper describes a pilot study to migrate the concept of linked data into the development of a domain-specific application, i.e. the vehicle repair support system. The set of commonly used concepts, including the part name of a car and the phenomenon term on the car repairing, are employed to build the linkage between data and documents distributed among different sources, leading to the fusion of documents and data across source boundaries. Then, we describe the approaches of semantic information retrieval to consume these linkages for value creation for companies. The experiments on two real-world data sets show that the proposed approaches outperform the best baseline 6.3-10.8% and 6.4-11.1% in terms of top five and top 10 precisions, respectively. We believe that our pilot study can serve as an important reference for the development of similar semantic applications in an enterprise environment.

Enhancing Reading Comprehension and Critical Thinking Skills of First Grade ESOL Students through the Use of Semantic Webbing.

ERIC Educational Resources Information Center

Kaufman, Madeline

In response to low reading scores among first grade students of English as a Second Language (ESL) in one inner-city school, the teaching techniques of semantic webbing and brainstorming were used to improve student reading skills. Subjects were eight first grade ESL students. Pretests were administered to assess student levels of reading…

A Metadata Model for E-Learning Coordination through Semantic Web Languages

ERIC Educational Resources Information Center

Elci, Atilla

2005-01-01

This paper reports on a study aiming to develop a metadata model for e-learning coordination based on semantic web languages. A survey of e-learning modes are done initially in order to identify content such as phases, activities, data schema, rules and relations, etc. relevant for a coordination model. In this respect, the study looks into the…

Entrez Neuron RDFa: a pragmatic Semantic Web application for data integration in neuroscience research

PubMed Central

Samwald, Matthias; Lim, Ernest; Masiar, Peter; Marenco, Luis; Chen, Huajun; Morse, Thomas; Mutalik, Pradeep; Shepherd, Gordon; Miller, Perry; Cheung, Kei-Hoi

2013-01-01

The amount of biomedical data available in Semantic Web formats has been rapidly growing in recent years. While these formats are machine-friendly, user-friendly web interfaces allowing easy querying of these data are typically lacking. We present “Entrez Neuron”, a pilot neuron-centric interface that allows for keyword-based queries against a coherent repository of OWL ontologies. These ontologies describe neuronal structures, physiology, mathematical models and microscopy images. The returned query results are organized hierarchically according to brain architecture. Where possible, the application makes use of entities from the Open Biomedical Ontologies (OBO) and the ‘HCLS knowledgebase’ developed by the W3C Interest Group for Health Care and Life Science. It makes use of the emerging RDFa standard to embed ontology fragments and semantic annotations within its HTML-based user interface. The application and underlying ontologies demonstrates how Semantic Web technologies can be used for information integration within a curated information repository and between curated information repositories. It also demonstrates how information integration can be accomplished on the client side, through simple copying and pasting of portions of documents that contain RDFa markup. PMID:19745321

An introduction to the Semantic Web for health sciences librarians*

PubMed Central

Robu, Ioana; Robu, Valentin; Thirion, Benoit

2006-01-01

Objectives: The paper (1) introduces health sciences librarians to the main concepts and principles of the Semantic Web (SW) and (2) briefly reviews a number of projects on the handling of biomedical information that uses SW technology. Methodology: The paper is structured into two main parts. “Semantic Web Technology” provides a high-level description, with examples, of the main standards and concepts: extensible markup language (XML), Resource Description Framework (RDF), RDF Schema (RDFS), ontologies, and their utility in information retrieval, concluding with mention of more advanced SW languages and their characteristics. “Semantic Web Applications and Research Projects in the Biomedical Field” is a brief review of the Unified Medical Language System (UMLS), Generalised Architecture for Languages, Encyclopedias and Nomenclatures in Medicine (GALEN), HealthCyberMap, LinkBase, and the thesaurus of the National Cancer Institute (NCI). The paper also mentions other benefits and by-products of the SW, citing projects related to them. Discussion and Conclusions: Some of the problems facing the SW vision are presented, especially the ways in which the librarians' expertise in organizing knowledge and in structuring information may contribute to SW projects. PMID:16636713

Executing SADI services in Galaxy.

PubMed

Aranguren, Mikel Egaña; González, Alejandro Rodríguez; Wilkinson, Mark D

2014-01-01

In recent years Galaxy has become a popular workflow management system in bioinformatics, due to its ease of installation, use and extension. The availability of Semantic Web-oriented tools in Galaxy, however, is limited. This is also the case for Semantic Web Services such as those provided by the SADI project, i.e. services that consume and produce RDF. Here we present SADI-Galaxy, a tool generator that deploys selected SADI Services as typical Galaxy tools. SADI-Galaxy is a Galaxy tool generator: through SADI-Galaxy, any SADI-compliant service becomes a Galaxy tool that can participate in other out-standing features of Galaxy such as data storage, history, workflow creation, and publication. Galaxy can also be used to execute and combine SADI services as it does with other Galaxy tools. Finally, we have semi-automated the packing and unpacking of data into RDF such that other Galaxy tools can easily be combined with SADI services, plugging the rich SADI Semantic Web Service environment into the popular Galaxy ecosystem. SADI-Galaxy bridges the gap between Galaxy, an easy to use but "static" workflow system with a wide user-base, and SADI, a sophisticated, semantic, discovery-based framework for Web Services, thus benefiting both user communities.

PREDOSE: A Semantic Web Platform for Drug Abuse Epidemiology using Social Media

PubMed Central

Cameron, Delroy; Smith, Gary A.; Daniulaityte, Raminta; Sheth, Amit P.; Dave, Drashti; Chen, Lu; Anand, Gaurish; Carlson, Robert; Watkins, Kera Z.; Falck, Russel

2013-01-01

Objectives The role of social media in biomedical knowledge mining, including clinical, medical and healthcare informatics, prescription drug abuse epidemiology and drug pharmacology, has become increasingly significant in recent years. Social media offers opportunities for people to share opinions and experiences freely in online communities, which may contribute information beyond the knowledge of domain professionals. This paper describes the development of a novel Semantic Web platform called PREDOSE (PREscription Drug abuse Online Surveillance and Epidemiology), which is designed to facilitate the epidemiologic study of prescription (and related) drug abuse practices using social media. PREDOSE uses web forum posts and domain knowledge, modeled in a manually created Drug Abuse Ontology (DAO) (pronounced dow), to facilitate the extraction of semantic information from User Generated Content (UGC). A combination of lexical, pattern-based and semantics-based techniques is used together with the domain knowledge to extract fine-grained semantic information from UGC. In a previous study, PREDOSE was used to obtain the datasets from which new knowledge in drug abuse research was derived. Here, we report on various platform enhancements, including an updated DAO, new components for relationship and triple extraction, and tools for content analysis, trend detection and emerging patterns exploration, which enhance the capabilities of the PREDOSE platform. Given these enhancements, PREDOSE is now more equipped to impact drug abuse research by alleviating traditional labor-intensive content analysis tasks. Methods Using custom web crawlers that scrape UGC from publicly available web forums, PREDOSE first automates the collection of web-based social media content for subsequent semantic annotation. The annotation scheme is modeled in the DAO, and includes domain specific knowledge such as prescription (and related) drugs, methods of preparation, side effects, routes of administration, etc. The DAO is also used to help recognize three types of data, namely: 1) entities, 2) relationships and 3) triples. PREDOSE then uses a combination of lexical and semantic-based techniques to extract entities and relationships from the scraped content, and a top-down approach for triple extraction that uses patterns expressed in the DAO. In addition, PREDOSE uses publicly available lexicons to identify initial sentiment expressions in text, and then a probabilistic optimization algorithm (from related research) to extract the final sentiment expressions. Together, these techniques enable the capture of fine-grained semantic information from UGC, and querying, search, trend analysis and overall content analysis of social media related to prescription drug abuse. Moreover, extracted data are also made available to domain experts for the creation of training and test sets for use in evaluation and refinements in information extraction techniques. Results A recent evaluation of the information extraction techniques applied in the PREDOSE platform indicates 85% precision and 72% recall in entity identification, on a manually created gold standard dataset. In another study, PREDOSE achieved 36% precision in relationship identification and 33% precision in triple extraction, through manual evaluation by domain experts. Given the complexity of the relationship and triple extraction tasks and the abstruse nature of social media texts, we interpret these as favorable initial results. Extracted semantic information is currently in use in an online discovery support system, by prescription drug abuse researchers at the Center for Interventions, Treatment and Addictions Research (CITAR) at Wright State University. Conclusion A comprehensive platform for entity, relationship, triple and sentiment extraction from such abstruse texts has never been developed for drug abuse research. PREDOSE has already demonstrated the importance of mining social media by providing data from which new findings in drug abuse research were uncovered. Given the recent platform enhancements, including the refined DAO, components for relationship and triple extraction, and tools for content, trend and emerging pattern analysis, it is expected that PREDOSE will play a significant role in advancing drug abuse epidemiology in future. PMID:23892295

Knowledge represented using RDF semantic network in the concept of semantic web

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lukasova, A., E-mail: alena.lukasova@osu.cz; Vajgl, M., E-mail: marek.vajgl@osu.cz; Zacek, M., E-mail: martin.zacek@osu.cz

The RDF(S) model has been declared as the basic model to capture knowledge of the semantic web. It provides a common and flexible way to decompose composed knowledge to elementary statements, which can be represented by RDF triples or by RDF graph vectors. From the logical point of view, elements of knowledge can be expressed using at most binary predicates, which can be converted to RDF-triples or graph vectors. However, it is not able to capture implicit knowledge representable by logical formulas. This contribution shows how existing approaches (semantic networks and clausal form logic) can be combined together with RDFmore » to obtain RDF-compatible system with ability to represent implicit knowledge and inference over knowledge base.« less

Ontology driven integration platform for clinical and translational research

PubMed Central

Mirhaji, Parsa; Zhu, Min; Vagnoni, Mattew; Bernstam, Elmer V; Zhang, Jiajie; Smith, Jack W

2009-01-01

Semantic Web technologies offer a promising framework for integration of disparate biomedical data. In this paper we present the semantic information integration platform under development at the Center for Clinical and Translational Sciences (CCTS) at the University of Texas Health Science Center at Houston (UTHSC-H) as part of our Clinical and Translational Science Award (CTSA) program. We utilize the Semantic Web technologies not only for integrating, repurposing and classification of multi-source clinical data, but also to construct a distributed environment for information sharing, and collaboration online. Service Oriented Architecture (SOA) is used to modularize and distribute reusable services in a dynamic and distributed environment. Components of the semantic solution and its overall architecture are described. PMID:19208190

The Semantic Learning Organization

ERIC Educational Resources Information Center

Sicilia, Miguel-Angel; Lytras, Miltiadis D.

2005-01-01

Purpose: The aim of this paper is introducing the concept of a "semantic learning organization" (SLO) as an extension of the concept of "learning organization" in the technological domain. Design/methodology/approach: The paper takes existing definitions and conceptualizations of both learning organizations and Semantic Web technology to develop…

Personalized Learning Objects Recommendation Based on the Semantic-Aware Discovery and the Learner Preference Pattern

ERIC Educational Resources Information Center

Wang, Tzone I; Tsai, Kun Hua; Lee, Ming Che; Chiu, Ti Kai

2007-01-01

With vigorous development of the Internet, especially the web page interaction technology, distant E-learning has become more and more realistic and popular. Digital courses may consist of many learning units or learning objects and, currently, many learning objects are created according to SCORM standard. It can be seen that, in the near future,…

Communicating and Sharing in the Semantic Web: An Examination of Social Media Risks, Consequences, and Attitudinal Awareness

ERIC Educational Resources Information Center

Buzzetto-More, Nicole; Johnson, Robert; Elobaid, Muna

2015-01-01

Empowered by and tethered to ubiquitous technologies, the current generation of youth yearns for opportunities to engage in self-expression and information sharing online with personal disclosure no longer governed by concepts of propriety and privacy. This raises issues about the unsafe online activities of teens and young adults. The following…

Integrating reasoning and clinical archetypes using OWL ontologies and SWRL rules.

PubMed

Lezcano, Leonardo; Sicilia, Miguel-Angel; Rodríguez-Solano, Carlos

2011-04-01

Semantic interoperability is essential to facilitate the computerized support for alerts, workflow management and evidence-based healthcare across heterogeneous electronic health record (EHR) systems. Clinical archetypes, which are formal definitions of specific clinical concepts defined as specializations of a generic reference (information) model, provide a mechanism to express data structures in a shared and interoperable way. However, currently available archetype languages do not provide direct support for mapping to formal ontologies and then exploiting reasoning on clinical knowledge, which are key ingredients of full semantic interoperability, as stated in the SemanticHEALTH report [1]. This paper reports on an approach to translate definitions expressed in the openEHR Archetype Definition Language (ADL) to a formal representation expressed using the Ontology Web Language (OWL). The formal representations are then integrated with rules expressed with Semantic Web Rule Language (SWRL) expressions, providing an approach to apply the SWRL rules to concrete instances of clinical data. Sharing the knowledge expressed in the form of rules is consistent with the philosophy of open sharing, encouraged by archetypes. Our approach also allows the reuse of formal knowledge, expressed through ontologies, and extends reuse to propositions of declarative knowledge, such as those encoded in clinical guidelines. This paper describes the ADL-to-OWL translation approach, describes the techniques to map archetypes to formal ontologies, and demonstrates how rules can be applied to the resulting representation. We provide examples taken from a patient safety alerting system to illustrate our approach. Copyright © 2010 Elsevier Inc. All rights reserved.

Enhancing acronym/abbreviation knowledge bases with semantic information.

PubMed

Torii, Manabu; Liu, Hongfang

2007-10-11

In the biomedical domain, a terminology knowledge base that associates acronyms/abbreviations (denoted as SFs) with the definitions (denoted as LFs) is highly needed. For the construction such terminology knowledge base, we investigate the feasibility to build a system automatically assigning semantic categories to LFs extracted from text. Given a collection of pairs (SF,LF) derived from text, we i) assess the coverage of LFs and pairs (SF,LF) in the UMLS and justify the need of a semantic category assignment system; and ii) automatically derive name phrases annotated with semantic category and construct a system using machine learning. Utilizing ADAM, an existing collection of (SF,LF) pairs extracted from MEDLINE, our system achieved an f-measure of 87% when assigning eight UMLS-based semantic groups to LFs. The system has been incorporated into a web interface which integrates SF knowledge from multiple SF knowledge bases. Web site: http://gauss.dbb.georgetown.edu/liblab/SFThesurus.

Semantic Analysis of Email Using Domain Ontologies and WordNet

NASA Technical Reports Server (NTRS)

Berrios, Daniel C.; Keller, Richard M.

2005-01-01

The problem of capturing and accessing knowledge in paper form has been supplanted by a problem of providing structure to vast amounts of electronic information. Systems that can construct semantic links for natural language documents like email messages automatically will be a crucial element of semantic email tools. We have designed an information extraction process that can leverage the knowledge already contained in an existing semantic web, recognizing references in email to existing nodes in a network of ontology instances by using linguistic knowledge and knowledge of the structure of the semantic web. We developed a heuristic score that uses several forms of evidence to detect references in email to existing nodes in the Semanticorganizer repository's network. While these scores cannot directly support automated probabilistic inference, they can be used to rank nodes by relevance and link those deemed most relevant to email messages.

A User-Centric Knowledge Creation Model in a Web of Object-Enabled Internet of Things Environment

PubMed Central

Kibria, Muhammad Golam; Fattah, Sheik Mohammad Mostakim; Jeong, Kwanghyeon; Chong, Ilyoung; Jeong, Youn-Kwae

2015-01-01

User-centric service features in a Web of Object-enabled Internet of Things environment can be provided by using a semantic ontology that classifies and integrates objects on the World Wide Web as well as shares and merges context-aware information and accumulated knowledge. The semantic ontology is applied on a Web of Object platform to virtualize the real world physical devices and information to form virtual objects that represent the features and capabilities of devices in the virtual world. Detailed information and functionalities of multiple virtual objects are combined with service rules to form composite virtual objects that offer context-aware knowledge-based services, where context awareness plays an important role in enabling automatic modification of the system to reconfigure the services based on the context. Converting the raw data into meaningful information and connecting the information to form the knowledge and storing and reusing the objects in the knowledge base can both be expressed by semantic ontology. In this paper, a knowledge creation model that synchronizes a service logistic model and a virtual world knowledge model on a Web of Object platform has been proposed. To realize the context-aware knowledge-based service creation and execution, a conceptual semantic ontology model has been developed and a prototype has been implemented for a use case scenario of emergency service. PMID:26393609

A User-Centric Knowledge Creation Model in a Web of Object-Enabled Internet of Things Environment.

PubMed

Kibria, Muhammad Golam; Fattah, Sheik Mohammad Mostakim; Jeong, Kwanghyeon; Chong, Ilyoung; Jeong, Youn-Kwae

2015-09-18

User-centric service features in a Web of Object-enabled Internet of Things environment can be provided by using a semantic ontology that classifies and integrates objects on the World Wide Web as well as shares and merges context-aware information and accumulated knowledge. The semantic ontology is applied on a Web of Object platform to virtualize the real world physical devices and information to form virtual objects that represent the features and capabilities of devices in the virtual world. Detailed information and functionalities of multiple virtual objects are combined with service rules to form composite virtual objects that offer context-aware knowledge-based services, where context awareness plays an important role in enabling automatic modification of the system to reconfigure the services based on the context. Converting the raw data into meaningful information and connecting the information to form the knowledge and storing and reusing the objects in the knowledge base can both be expressed by semantic ontology. In this paper, a knowledge creation model that synchronizes a service logistic model and a virtual world knowledge model on a Web of Object platform has been proposed. To realize the context-aware knowledge-based service creation and execution, a conceptual semantic ontology model has been developed and a prototype has been implemented for a use case scenario of emergency service.

Annotating Atomic Components of Papers in Digital Libraries: The Semantic and Social Web Heading towards a Living Document Supporting eSciences

NASA Astrophysics Data System (ADS)

García Castro, Alexander; García-Castro, Leyla Jael; Labarga, Alberto; Giraldo, Olga; Montaña, César; O'Neil, Kieran; Bateman, John A.

Rather than a document that is being constantly re-written as in the wiki approach, the Living Document (LD) is one that acts as a document router, operating by means of structured and organized social tagging and existing ontologies. It offers an environment where users can manage papers and related information, share their knowledge with their peers and discover hidden associations among the shared knowledge. The LD builds upon both the Semantic Web, which values the integration of well-structured data, and the Social Web, which aims to facilitate interaction amongst people by means of user-generated content. In this vein, the LD is similar to a social networking system, with users as central nodes in the network, with the difference that interaction is focused on papers rather than people. Papers, with their ability to represent research interests, expertise, affiliations, and links to web based tools and databanks, represent a central axis for interaction amongst users. To begin to show the potential of this vision, we have implemented a novel web prototype that enables researchers to accomplish three activities central to the Semantic Web vision: organizing, sharing and discovering. Availability: http://www.scientifik.info/

Bim-Gis Integrated Geospatial Information Model Using Semantic Web and Rdf Graphs

NASA Astrophysics Data System (ADS)

Hor, A.-H.; Jadidi, A.; Sohn, G.

2016-06-01

In recent years, 3D virtual indoor/outdoor urban modelling becomes a key spatial information framework for many civil and engineering applications such as evacuation planning, emergency and facility management. For accomplishing such sophisticate decision tasks, there is a large demands for building multi-scale and multi-sourced 3D urban models. Currently, Building Information Model (BIM) and Geographical Information Systems (GIS) are broadly used as the modelling sources. However, data sharing and exchanging information between two modelling domains is still a huge challenge; while the syntactic or semantic approaches do not fully provide exchanging of rich semantic and geometric information of BIM into GIS or vice-versa. This paper proposes a novel approach for integrating BIM and GIS using semantic web technologies and Resources Description Framework (RDF) graphs. The novelty of the proposed solution comes from the benefits of integrating BIM and GIS technologies into one unified model, so-called Integrated Geospatial Information Model (IGIM). The proposed approach consists of three main modules: BIM-RDF and GIS-RDF graphs construction, integrating of two RDF graphs, and query of information through IGIM-RDF graph using SPARQL. The IGIM generates queries from both the BIM and GIS RDF graphs resulting a semantically integrated model with entities representing both BIM classes and GIS feature objects with respect to the target-client application. The linkage between BIM-RDF and GIS-RDF is achieved through SPARQL endpoints and defined by a query using set of datasets and entity classes with complementary properties, relationships and geometries. To validate the proposed approach and its performance, a case study was also tested using IGIM system design.

WikiHyperGlossary (WHG): an information literacy technology for chemistry documents.

PubMed

Bauer, Michael A; Berleant, Daniel; Cornell, Andrew P; Belford, Robert E

2015-01-01

The WikiHyperGlossary is an information literacy technology that was created to enhance reading comprehension of documents by connecting them to socially generated multimedia definitions as well as semantically relevant data. The WikiHyperGlossary enhances reading comprehension by using the lexicon of a discipline to generate dynamic links in a document to external resources that can provide implicit information the document did not explicitly provide. Currently, the most common method to acquire additional information when reading a document is to access a search engine and browse the web. This may lead to skimming of multiple documents with the novice actually never returning to the original document of interest. The WikiHyperGlossary automatically brings information to the user within the current document they are reading, enhancing the potential for deeper document understanding. The WikiHyperGlossary allows users to submit a web URL or text to be processed against a chosen lexicon, returning the document with tagged terms. The selection of a tagged term results in the appearance of the WikiHyperGlossary Portlet containing a definition, and depending on the type of word, tabs to additional information and resources. Current types of content include multimedia enhanced definitions, ChemSpider query results, 3D molecular structures, and 2D editable structures connected to ChemSpider queries. Existing glossaries can be bulk uploaded, locked for editing and associated with multiple social generated definitions. The WikiHyperGlossary leverages both social and semantic web technologies to bring relevant information to a document. This can not only aid reading comprehension, but increases the users' ability to obtain additional information within the document. We have demonstrated a molecular editor enabled knowledge framework that can result in a semantic web inductive reasoning process, and integration of the WikiHyperGlossary into other software technologies, like the Jikitou Biomedical Question and Answer system. Although this work was developed in the chemical sciences and took advantage of open science resources and initiatives, the technology is extensible to other knowledge domains. Through the DeepLit (Deeper Literacy: Connecting Documents to Data and Discourse) startup, we seek to extend WikiHyperGlossary technologies to other knowledge domains, and integrate them into other knowledge acquisition workflows.

Interleaving Semantic Web Reasoning and Service Discovery to Enforce Context-Sensitive Security and Privacy Policies

DTIC Science & Technology

2005-07-01

policies in pervasive computing environments. In this context, the owner of information sources (e.g. user, sensor, application, or organization...work in decentralized trust management and semantic web technologies . Section 3 introduces an Information Disclosure Agent architecture for...Norman Sadeh July 2005 CMU-ISRI-05-113 School of Computer Science, Carnegie Mellon University 5000 Forbes Avenue, Pittsburgh, PA, 15213

The New Challenges for E-learning: The Educational Semantic Web

ERIC Educational Resources Information Center

Aroyo, Lora; Dicheva, Darina

2004-01-01

The big question for many researchers in the area of educational systems now is what is the next step in the evolution of e-learning? Are we finally moving from a scattered intelligence to a coherent space of collaborative intelligence? How close we are to the vision of the Educational Semantic Web and what do we need to do in order to realize it?…

Effects of Semantic Web Based Learning on Pre-Service Teachers' ICT Learning Achievement and Satisfaction

ERIC Educational Resources Information Center

Karalar, Halit; Korucu, Agah Tugrul

2016-01-01

Although the Semantic Web offers many opportunities for learners, effects of it in the classroom is not well known. Therefore, in this study explanations have been stated as how the learning objects defined by means of using the terminology in a developed ontology and kept in objects repository should be presented to learners with the aim of…

Semantic Document Model to Enhance Data and Knowledge Interoperability

NASA Astrophysics Data System (ADS)

Nešić, Saša

To enable document data and knowledge to be efficiently shared and reused across application, enterprise, and community boundaries, desktop documents should be completely open and queryable resources, whose data and knowledge are represented in a form understandable to both humans and machines. At the same time, these are the requirements that desktop documents need to satisfy in order to contribute to the visions of the Semantic Web. With the aim of achieving this goal, we have developed the Semantic Document Model (SDM), which turns desktop documents into Semantic Documents as uniquely identified and semantically annotated composite resources, that can be instantiated into human-readable (HR) and machine-processable (MP) forms. In this paper, we present the SDM along with an RDF and ontology-based solution for the MP document instance. Moreover, on top of the proposed model, we have built the Semantic Document Management System (SDMS), which provides a set of services that exploit the model. As an application example that takes advantage of SDMS services, we have extended MS Office with a set of tools that enables users to transform MS Office documents (e.g., MS Word and MS PowerPoint) into Semantic Documents, and to search local and distant semantic document repositories for document content units (CUs) over Semantic Web protocols.

The MMI Semantic Framework: Rosetta Stones for Earth Sciences

NASA Astrophysics Data System (ADS)

Rueda, C.; Bermudez, L. E.; Graybeal, J.; Alexander, P.

2009-12-01

Semantic interoperability—the exchange of meaning among computer systems—is needed to successfully share data in Ocean Science and across all Earth sciences. The best approach toward semantic interoperability requires a designed framework, and operationally tested tools and infrastructure within that framework. Currently available technologies make a scientific semantic framework feasible, but its development requires sustainable architectural vision and development processes. This presentation outlines the MMI Semantic Framework, including recent progress on it and its client applications. The MMI Semantic Framework consists of tools, infrastructure, and operational and community procedures and best practices, to meet short-term and long-term semantic interoperability goals. The design and prioritization of the semantic framework capabilities are based on real-world scenarios in Earth observation systems. We describe some key uses cases, as well as the associated requirements for building the overall infrastructure, which is realized through the MMI Ontology Registry and Repository. This system includes support for community creation and sharing of semantic content, ontology registration, version management, and seamless integration of user-friendly tools and application programming interfaces. The presentation describes the architectural components for semantic mediation, registry and repository for vocabularies, ontology, and term mappings. We show how the technologies and approaches in the framework can address community needs for managing and exchanging semantic information. We will demonstrate how different types of users and client applications exploit the tools and services for data aggregation, visualization, archiving, and integration. Specific examples from OOSTethys (http://www.oostethys.org) and the Ocean Observatories Initiative Cyberinfrastructure (http://www.oceanobservatories.org) will be cited. Finally, we show how semantic augmentation of web services standards could be performed using framework tools.

Can social semantic web techniques foster collaborative curriculum mapping in medicine?

PubMed

Spreckelsen, Cord; Finsterer, Sonja; Cremer, Jan; Schenkat, Hennig

2013-08-15

Curriculum mapping, which is aimed at the systematic realignment of the planned, taught, and learned curriculum, is considered a challenging and ongoing effort in medical education. Second-generation curriculum managing systems foster knowledge management processes including curriculum mapping in order to give comprehensive support to learners, teachers, and administrators. The large quantity of custom-built software in this field indicates a shortcoming of available IT tools and standards. The project reported here aims at the systematic adoption of techniques and standards of the Social Semantic Web to implement collaborative curriculum mapping for a complete medical model curriculum. A semantic MediaWiki (SMW)-based Web application has been introduced as a platform for the elicitation and revision process of the Aachen Catalogue of Learning Objectives (ACLO). The semantic wiki uses a domain model of the curricular context and offers structured (form-based) data entry, multiple views, structured querying, semantic indexing, and commenting for learning objectives ("LOs"). Semantic indexing of learning objectives relies on both a controlled vocabulary of international medical classifications (ICD, MeSH) and a folksonomy maintained by the users. An additional module supporting the global checking of consistency complements the semantic wiki. Statements of the Object Constraint Language define the consistency criteria. We evaluated the application by a scenario-based formative usability study, where the participants solved tasks in the (fictional) context of 7 typical situations and answered a questionnaire containing Likert-scaled items and free-text questions. At present, ACLO contains roughly 5350 operational (ie, specific and measurable) objectives acquired during the last 25 months. The wiki-based user interface uses 13 online forms for data entry and 4 online forms for flexible searches of LOs, and all the forms are accessible by standard Web browsers. The formative usability study yielded positive results (median rating of 2 ("good") in all 7 general usability items) and produced valuable qualitative feedback, especially concerning navigation and comprehensibility. Although not asked to, the participants (n=5) detected critical aspects of the curriculum (similar learning objectives addressed repeatedly and missing objectives), thus proving the system's ability to support curriculum revision. The SMW-based approach enabled an agile implementation of computer-supported knowledge management. The approach, based on standard Social Semantic Web formats and technology, represents a feasible and effectively applicable compromise between answering to the individual requirements of curriculum management at a particular medical school and using proprietary systems.

Semantic-JSON: a lightweight web service interface for Semantic Web contents integrating multiple life science databases

PubMed Central

Kobayashi, Norio; Ishii, Manabu; Takahashi, Satoshi; Mochizuki, Yoshiki; Matsushima, Akihiro; Toyoda, Tetsuro

2011-01-01

Global cloud frameworks for bioinformatics research databases become huge and heterogeneous; solutions face various diametric challenges comprising cross-integration, retrieval, security and openness. To address this, as of March 2011 organizations including RIKEN published 192 mammalian, plant and protein life sciences databases having 8.2 million data records, integrated as Linked Open or Private Data (LOD/LPD) using SciNetS.org, the Scientists' Networking System. The huge quantity of linked data this database integration framework covers is based on the Semantic Web, where researchers collaborate by managing metadata across public and private databases in a secured data space. This outstripped the data query capacity of existing interface tools like SPARQL. Actual research also requires specialized tools for data analysis using raw original data. To solve these challenges, in December 2009 we developed the lightweight Semantic-JSON interface to access each fragment of linked and raw life sciences data securely under the control of programming languages popularly used by bioinformaticians such as Perl and Ruby. Researchers successfully used the interface across 28 million semantic relationships for biological applications including genome design, sequence processing, inference over phenotype databases, full-text search indexing and human-readable contents like ontology and LOD tree viewers. Semantic-JSON services of SciNetS.org are provided at http://semanticjson.org. PMID:21632604

Smarter Earth Science Data System

NASA Technical Reports Server (NTRS)

Huang, Thomas

2013-01-01

The explosive growth in Earth observational data in the recent decade demands a better method of interoperability across heterogeneous systems. The Earth science data system community has mastered the art in storing large volume of observational data, but it is still unclear how this traditional method scale over time as we are entering the age of Big Data. Indexed search solutions such as Apache Solr (Smiley and Pugh, 2011) provides fast, scalable search via keyword or phases without any reasoning or inference. The modern search solutions such as Googles Knowledge Graph (Singhal, 2012) and Microsoft Bing, all utilize semantic reasoning to improve its accuracy in searches. The Earth science user community is demanding for an intelligent solution to help them finding the right data for their researches. The Ontological System for Context Artifacts and Resources (OSCAR) (Huang et al., 2012), was created in response to the DARPA Adaptive Vehicle Make (AVM) programs need for an intelligent context models management system to empower its terrain simulation subsystem. The core component of OSCAR is the Environmental Context Ontology (ECO) is built using the Semantic Web for Earth and Environmental Terminology (SWEET) (Raskin and Pan, 2005). This paper presents the current data archival methodology within a NASA Earth science data centers and discuss using semantic web to improve the way we capture and serve data to our users.

Semantic-Aware Components and Services of ActiveMath

ERIC Educational Resources Information Center

Melis, Erica; Goguadze, Giorgi; Homik, Martin; Libbrecht, Paul; Ullrich, Carsten; Winterstein, Stefan

2006-01-01

ActiveMath is a complex web-based adaptive learning environment with a number of components and interactive learning tools. The basis for handling semantics of learning content is provided by its semantic (mathematics) content markup, which is additionally annotated with educational metadata. Several components, tools and external services can…

Kernel Methods for Mining Instance Data in Ontologies

NASA Astrophysics Data System (ADS)

Bloehdorn, Stephan; Sure, York

The amount of ontologies and meta data available on the Web is constantly growing. The successful application of machine learning techniques for learning of ontologies from textual data, i.e. mining for the Semantic Web, contributes to this trend. However, no principal approaches exist so far for mining from the Semantic Web. We investigate how machine learning algorithms can be made amenable for directly taking advantage of the rich knowledge expressed in ontologies and associated instance data. Kernel methods have been successfully employed in various learning tasks and provide a clean framework for interfacing between non-vectorial data and machine learning algorithms. In this spirit, we express the problem of mining instances in ontologies as the problem of defining valid corresponding kernels. We present a principled framework for designing such kernels by means of decomposing the kernel computation into specialized kernels for selected characteristics of an ontology which can be flexibly assembled and tuned. Initial experiments on real world Semantic Web data enjoy promising results and show the usefulness of our approach.

Web information retrieval based on ontology

NASA Astrophysics Data System (ADS)

Zhang, Jian

2013-03-01

The purpose of the Information Retrieval (IR) is to find a set of documents that are relevant for a specific information need of a user. Traditional Information Retrieval model commonly used in commercial search engine is based on keyword indexing system and Boolean logic queries. One big drawback of traditional information retrieval is that they typically retrieve information without an explicitly defined domain of interest to the users so that a lot of no relevance information returns to users, which burden the user to pick up useful answer from these no relevance results. In order to tackle this issue, many semantic web information retrieval models have been proposed recently. The main advantage of Semantic Web is to enhance search mechanisms with the use of Ontology's mechanisms. In this paper, we present our approach to personalize web search engine based on ontology. In addition, key techniques are also discussed in our paper. Compared to previous research, our works concentrate on the semantic similarity and the whole process including query submission and information annotation.

Problems of teaching students to use the featured technologies in the area of semantic web

NASA Astrophysics Data System (ADS)

Klimov, V. V.; Chernyshov, A. A.; Balandina, A. I.; Kostkina, A. D.

2017-01-01

The following paper contains the description of up-to-date technologies in the area of web-services development, service-oriented architecture and the Semantic Web. The paper contains the analysis of the most popular and widespread technologies and methods in the semantic web area which are used in the developed educational course. In the paper, we also describe the problem of teaching students to use these technologies and specify conditions for the creation of the learning and development course. We also describe the main exercise for personal work and skills, which all the students learning this course have to gain. Moreover, in the paper we specify the problem with software which students are going to use while learning this course. In order to solve this problem, we introduce the developing system which will be used to support the laboratory works. For this moment this system supports only the fourth work execution, but our following plans contain the expansion of the system in order to support the leftover works.

Development of intelligent semantic search system for rubber research data in Thailand

NASA Astrophysics Data System (ADS)

Kaewboonma, Nattapong; Panawong, Jirapong; Pianhanuruk, Ekkawit; Buranarach, Marut

2017-10-01

The rubber production of Thailand increased not only by strong demand from the world market, but was also stimulated strongly through the replanting program of the Thai Government from 1961 onwards. With the continuous growth of rubber research data volume on the Web, the search for information has become a challenging task. Ontologies are used to improve the accuracy of information retrieval from the web by incorporating a degree of semantic analysis during the search. In this context, we propose an intelligent semantic search system for rubber research data in Thailand. The research methods included 1) analyzing domain knowledge, 2) ontologies development, and 3) intelligent semantic search system development to curate research data in trusted digital repositories may be shared among the wider Thailand rubber research community.

Model-based document categorization employing semantic pattern analysis and local structure clustering

NASA Astrophysics Data System (ADS)

Fume, Kosei; Ishitani, Yasuto

2008-01-01

We propose a document categorization method based on a document model that can be defined externally for each task and that categorizes Web content or business documents into a target category in accordance with the similarity of the model. The main feature of the proposed method consists of two aspects of semantics extraction from an input document. The semantics of terms are extracted by the semantic pattern analysis and implicit meanings of document substructure are specified by a bottom-up text clustering technique focusing on the similarity of text line attributes. We have constructed a system based on the proposed method for trial purposes. The experimental results show that the system achieves more than 80% classification accuracy in categorizing Web content and business documents into 15 or 70 categories.

Cheminformatics and the Semantic Web: adding value with linked data and enhanced provenance

PubMed Central

Frey, Jeremy G; Bird, Colin L

2013-01-01

Cheminformatics is evolving from being a field of study associated primarily with drug discovery into a discipline that embraces the distribution, management, access, and sharing of chemical data. The relationship with the related subject of bioinformatics is becoming stronger and better defined, owing to the influence of Semantic Web technologies, which enable researchers to integrate heterogeneous sources of chemical, biochemical, biological, and medical information. These developments depend on a range of factors: the principles of chemical identifiers and their role in relationships between chemical and biological entities; the importance of preserving provenance and properly curated metadata; and an understanding of the contribution that the Semantic Web can make at all stages of the research lifecycle. The movements toward open access, open source, and open collaboration all contribute to progress toward the goals of integration. PMID:24432050

Graph Mining Meets the Semantic Web

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Sangkeun; Sukumar, Sreenivas R; Lim, Seung-Hwan

The Resource Description Framework (RDF) and SPARQL Protocol and RDF Query Language (SPARQL) were introduced about a decade ago to enable flexible schema-free data interchange on the Semantic Web. Today, data scientists use the framework as a scalable graph representation for integrating, querying, exploring and analyzing data sets hosted at different sources. With increasing adoption, the need for graph mining capabilities for the Semantic Web has emerged. We address that need through implementation of three popular iterative Graph Mining algorithms (Triangle count, Connected component analysis, and PageRank). We implement these algorithms as SPARQL queries, wrapped within Python scripts. We evaluatemore » the performance of our implementation on 6 real world data sets and show graph mining algorithms (that have a linear-algebra formulation) can indeed be unleashed on data represented as RDF graphs using the SPARQL query interface.« less

Automatic Generation of Mashups for Personalized Commerce in Digital TV by Semantic Reasoning

NASA Astrophysics Data System (ADS)

Blanco-Fernández, Yolanda; López-Nores, Martín; Pazos-Arias, José J.; Martín-Vicente, Manuela I.

The evolution of information technologies is consolidating recommender systems as essential tools in e-commerce. To date, these systems have focused on discovering the items that best match the preferences, interests and needs of individual users, to end up listing those items by decreasing relevance in some menus. In this paper, we propose extending the current scope of recommender systems to better support trading activities, by automatically generating interactive applications that provide the users with personalized commercial functionalities related to the selected items. We explore this idea in the context of Digital TV advertising, with a system that brings together semantic reasoning techniques and new architectural solutions for web services and mashups.

A-DaGO-Fun: an adaptable Gene Ontology semantic similarity-based functional analysis tool.

PubMed

Mazandu, Gaston K; Chimusa, Emile R; Mbiyavanga, Mamana; Mulder, Nicola J

2016-02-01

Gene Ontology (GO) semantic similarity measures are being used for biological knowledge discovery based on GO annotations by integrating biological information contained in the GO structure into data analyses. To empower users to quickly compute, manipulate and explore these measures, we introduce A-DaGO-Fun (ADaptable Gene Ontology semantic similarity-based Functional analysis). It is a portable software package integrating all known GO information content-based semantic similarity measures and relevant biological applications associated with these measures. A-DaGO-Fun has the advantage not only of handling datasets from the current high-throughput genome-wide applications, but also allowing users to choose the most relevant semantic similarity approach for their biological applications and to adapt a given module to their needs. A-DaGO-Fun is freely available to the research community at http://web.cbio.uct.ac.za/ITGOM/adagofun. It is implemented in Linux using Python under free software (GNU General Public Licence). gmazandu@cbio.uct.ac.za or Nicola.Mulder@uct.ac.za Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Automatic geospatial information Web service composition based on ontology interface matching

NASA Astrophysics Data System (ADS)

Xu, Xianbin; Wu, Qunyong; Wang, Qinmin

2008-10-01

With Web services technology the functions of WebGIS can be presented as a kind of geospatial information service, and helped to overcome the limitation of the information-isolated situation in geospatial information sharing field. Thus Geospatial Information Web service composition, which conglomerates outsourced services working in tandem to offer value-added service, plays the key role in fully taking advantage of geospatial information services. This paper proposes an automatic geospatial information web service composition algorithm that employed the ontology dictionary WordNet to analyze semantic distances among the interfaces. Through making matching between input/output parameters and the semantic meaning of pairs of service interfaces, a geospatial information web service chain can be created from a number of candidate services. A practice of the algorithm is also proposed and the result of it shows the feasibility of this algorithm and the great promise in the emerging demand for geospatial information web service composition.

Produce and Consume Linked Data with Drupal!

NASA Astrophysics Data System (ADS)

Corlosquet, Stéphane; Delbru, Renaud; Clark, Tim; Polleres, Axel; Decker, Stefan

Currently a large number of Web sites are driven by Content Management Systems (CMS) which manage textual and multimedia content but also - inherently - carry valuable information about a site's structure and content model. Exposing this structured information to the Web of Data has so far required considerable expertise in RDF and OWL modelling and additional programming effort. In this paper we tackle one of the most popular CMS: Drupal. We enable site administrators to export their site content model and data to the Web of Data without requiring extensive knowledge on Semantic Web technologies. Our modules create RDFa annotations and - optionally - a SPARQL endpoint for any Drupal site out of the box. Likewise, we add the means to map the site data to existing ontologies on the Web with a search interface to find commonly used ontology terms. We also allow a Drupal site administrator to include existing RDF data from remote SPARQL endpoints on the Web in the site. When brought together, these features allow networked RDF Drupal sites that reuse and enrich Linked Data. We finally discuss the adoption of our modules and report on a use case in the biomedical field and the current status of its deployment.

Improving User Experience by Taking Advance of Semantic Information of Microformats on Municipal Websites

NASA Astrophysics Data System (ADS)

Rodríguez, Rocío; Vera, Pablo; Estevez, Elsa; Giulianelli, Daniel; Welicki, León; Trigueros, Artemisa

This research regards about the use of microformats as a tool to add semantic information to government web sites. The use of microformats allows the developer to add different resources such as maps, calendars, etc, in an easy way. The paper also shows a survey of the already existing microformats and which of them are useful to be applied to government web sites.

Semantic Web and Inferencing Technologies for Department of Defense Systems

DTIC Science & Technology

2014-10-01

contact report for a specific type of aircraft . Intra-domain-specific metadata in the threat data domain might be used to categorize the contact...DEFENSE SYSTEMS by Duane Davis October 2014 Approved for public release; distribution is unlimited Prepared for: The NPS Center for Multi-INT...TITLE AND SUBTITLE Semantic Web and Inferencing Technologies for Department of Defense Systems 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c

Semantic Web repositories for genomics data using the eXframe platform.

PubMed

Merrill, Emily; Corlosquet, Stéphane; Ciccarese, Paolo; Clark, Tim; Das, Sudeshna

2014-01-01

With the advent of inexpensive assay technologies, there has been an unprecedented growth in genomics data as well as the number of databases in which it is stored. In these databases, sample annotation using ontologies and controlled vocabularies is becoming more common. However, the annotation is rarely available as Linked Data, in a machine-readable format, or for standardized queries using SPARQL. This makes large-scale reuse, or integration with other knowledge bases very difficult. To address this challenge, we have developed the second generation of our eXframe platform, a reusable framework for creating online repositories of genomics experiments. This second generation model now publishes Semantic Web data. To accomplish this, we created an experiment model that covers provenance, citations, external links, assays, biomaterials used in the experiment, and the data collected during the process. The elements of our model are mapped to classes and properties from various established biomedical ontologies. Resource Description Framework (RDF) data is automatically produced using these mappings and indexed in an RDF store with a built-in Sparql Protocol and RDF Query Language (SPARQL) endpoint. Using the open-source eXframe software, institutions and laboratories can create Semantic Web repositories of their experiments, integrate it with heterogeneous resources and make it interoperable with the vast Semantic Web of biomedical knowledge.

Integrating Statistical Machine Learning in a Semantic Sensor Web for Proactive Monitoring and Control.

PubMed

Adeleke, Jude Adekunle; Moodley, Deshendran; Rens, Gavin; Adewumi, Aderemi Oluyinka

2017-04-09

Proactive monitoring and control of our natural and built environments is important in various application scenarios. Semantic Sensor Web technologies have been well researched and used for environmental monitoring applications to expose sensor data for analysis in order to provide responsive actions in situations of interest. While these applications provide quick response to situations, to minimize their unwanted effects, research efforts are still necessary to provide techniques that can anticipate the future to support proactive control, such that unwanted situations can be averted altogether. This study integrates a statistical machine learning based predictive model in a Semantic Sensor Web using stream reasoning. The approach is evaluated in an indoor air quality monitoring case study. A sliding window approach that employs the Multilayer Perceptron model to predict short term PM 2 . 5 pollution situations is integrated into the proactive monitoring and control framework. Results show that the proposed approach can effectively predict short term PM 2 . 5 pollution situations: precision of up to 0.86 and sensitivity of up to 0.85 is achieved over half hour prediction horizons, making it possible for the system to warn occupants or even to autonomously avert the predicted pollution situations within the context of Semantic Sensor Web.

Integrating Statistical Machine Learning in a Semantic Sensor Web for Proactive Monitoring and Control

PubMed Central

Adeleke, Jude Adekunle; Moodley, Deshendran; Rens, Gavin; Adewumi, Aderemi Oluyinka

2017-01-01

Proactive monitoring and control of our natural and built environments is important in various application scenarios. Semantic Sensor Web technologies have been well researched and used for environmental monitoring applications to expose sensor data for analysis in order to provide responsive actions in situations of interest. While these applications provide quick response to situations, to minimize their unwanted effects, research efforts are still necessary to provide techniques that can anticipate the future to support proactive control, such that unwanted situations can be averted altogether. This study integrates a statistical machine learning based predictive model in a Semantic Sensor Web using stream reasoning. The approach is evaluated in an indoor air quality monitoring case study. A sliding window approach that employs the Multilayer Perceptron model to predict short term PM2.5 pollution situations is integrated into the proactive monitoring and control framework. Results show that the proposed approach can effectively predict short term PM2.5 pollution situations: precision of up to 0.86 and sensitivity of up to 0.85 is achieved over half hour prediction horizons, making it possible for the system to warn occupants or even to autonomously avert the predicted pollution situations within the context of Semantic Sensor Web. PMID:28397776

CHIP Demonstrator: Semantics-Driven Recommendations and Museum Tour Generation

NASA Astrophysics Data System (ADS)

Aroyo, Lora; Stash, Natalia; Wang, Yiwen; Gorgels, Peter; Rutledge, Lloyd

The main objective of the CHIP project is to demonstrate how Semantic Web technologies can be deployed to provide personalized access to digital museum collections. We illustrate our approach with the digital database ARIA of the Rijksmuseum Amsterdam. For the semantic enrichment of the Rijksmuseum ARIA database we collaborated with the CATCH STITCH project to produce mappings to Iconclass, and with the MultimediaN E-culture project to produce the RDF/OWL of the ARIA and Adlib databases. The main focus of CHIP is on exploring the potential of applying adaptation techniques to provide personalized experience for the museum visitors both on the Web site and in the museum.

Supporting open collaboration in science through explicit and linked semantic description of processes

USGS Publications Warehouse

Gil, Yolanda; Michel, Felix; Ratnakar, Varun; Read, Jordan S.; Hauder, Matheus; Duffy, Christopher; Hanson, Paul C.; Dugan, Hilary

2015-01-01

The Web was originally developed to support collaboration in science. Although scientists benefit from many forms of collaboration on the Web (e.g., blogs, wikis, forums, code sharing, etc.), most collaborative projects are coordinated over email, phone calls, and in-person meetings. Our goal is to develop a collaborative infrastructure for scientists to work on complex science questions that require multi-disciplinary contributions to gather and analyze data, that cannot occur without significant coordination to synthesize findings, and that grow organically to accommodate new contributors as needed as the work evolves over time. Our approach is to develop an organic data science framework based on a task-centered organization of the collaboration, includes principles from social sciences for successful on-line communities, and exposes an open science process. Our approach is implemented as an extension of a semantic wiki platform, and captures formal representations of task decomposition structures, relations between tasks and users, and other properties of tasks, data, and other relevant science objects. All these entities are captured through the semantic wiki user interface, represented as semantic web objects, and exported as linked data.

Unifying Access to National Hydrologic Data Repositories via Web Services

NASA Astrophysics Data System (ADS)

Valentine, D. W.; Jennings, B.; Zaslavsky, I.; Maidment, D. R.

2006-12-01

The CUAHSI hydrologic information system (HIS) is designed to be a live, multiscale web portal system for accessing, querying, visualizing, and publishing distributed hydrologic observation data and models for any location or region in the United States. The HIS design follows the principles of open service oriented architecture, i.e. system components are represented as web services with well defined standard service APIs. WaterOneFlow web services are the main component of the design. The currently available services have been completely re-written compared to the previous version, and provide programmatic access to USGS NWIS. (steam flow, groundwater and water quality repositories), DAYMET daily observations, NASA MODIS, and Unidata NAM streams, with several additional web service wrappers being added (EPA STORET, NCDC and others.). Different repositories of hydrologic data use different vocabularies, and support different types of query access. Resolving semantic and structural heterogeneities across different hydrologic observation archives and distilling a generic set of service signatures is one of the main scalability challenges in this project, and a requirement in our web service design. To accomplish the uniformity of the web services API, data repositories are modeled following the CUAHSI Observation Data Model. The web service responses are document-based, and use an XML schema to express the semantics in a standard format. Access to station metadata is provided via web service methods, GetSites, GetSiteInfo and GetVariableInfo. The methdods form the foundation of CUAHSI HIS discovery interface and may execute over locally-stored metadata or request the information from remote repositories directly. Observation values are retrieved via a generic GetValues method which is executed against national data repositories. The service is implemented in ASP.Net, and other providers are implementing WaterOneFlow services in java. Reference implementation of WaterOneFlow web services is available. More information about the ongoing development of CUAHSI HIS is available from http://www.cuahsi.org/his/.

Leveraging Pattern Semantics for Extracting Entities in Enterprises

PubMed Central

Tao, Fangbo; Zhao, Bo; Fuxman, Ariel; Li, Yang; Han, Jiawei

2015-01-01

Entity Extraction is a process of identifying meaningful entities from text documents. In enterprises, extracting entities improves enterprise efficiency by facilitating numerous applications, including search, recommendation, etc. However, the problem is particularly challenging on enterprise domains due to several reasons. First, the lack of redundancy of enterprise entities makes previous web-based systems like NELL and OpenIE not effective, since using only high-precision/low-recall patterns like those systems would miss the majority of sparse enterprise entities, while using more low-precision patterns in sparse setting also introduces noise drastically. Second, semantic drift is common in enterprises (“Blue” refers to “Windows Blue”), such that public signals from the web cannot be directly applied on entities. Moreover, many internal entities never appear on the web. Sparse internal signals are the only source for discovering them. To address these challenges, we propose an end-to-end framework for extracting entities in enterprises, taking the input of enterprise corpus and limited seeds to generate a high-quality entity collection as output. We introduce the novel concept of Semantic Pattern Graph to leverage public signals to understand the underlying semantics of lexical patterns, reinforce pattern evaluation using mined semantics, and yield more accurate and complete entities. Experiments on Microsoft enterprise data show the effectiveness of our approach. PMID:26705540

Leveraging Pattern Semantics for Extracting Entities in Enterprises.

PubMed

Tao, Fangbo; Zhao, Bo; Fuxman, Ariel; Li, Yang; Han, Jiawei

2015-05-01

Entity Extraction is a process of identifying meaningful entities from text documents. In enterprises, extracting entities improves enterprise efficiency by facilitating numerous applications, including search, recommendation, etc. However, the problem is particularly challenging on enterprise domains due to several reasons. First, the lack of redundancy of enterprise entities makes previous web-based systems like NELL and OpenIE not effective, since using only high-precision/low-recall patterns like those systems would miss the majority of sparse enterprise entities, while using more low-precision patterns in sparse setting also introduces noise drastically. Second, semantic drift is common in enterprises ("Blue" refers to "Windows Blue"), such that public signals from the web cannot be directly applied on entities. Moreover, many internal entities never appear on the web. Sparse internal signals are the only source for discovering them. To address these challenges, we propose an end-to-end framework for extracting entities in enterprises, taking the input of enterprise corpus and limited seeds to generate a high-quality entity collection as output. We introduce the novel concept of Semantic Pattern Graph to leverage public signals to understand the underlying semantics of lexical patterns, reinforce pattern evaluation using mined semantics, and yield more accurate and complete entities. Experiments on Microsoft enterprise data show the effectiveness of our approach.

Towards a Semantic Web of Things: A Hybrid Semantic Annotation, Extraction, and Reasoning Framework for Cyber-Physical System.

PubMed

Wu, Zhenyu; Xu, Yuan; Yang, Yunong; Zhang, Chunhong; Zhu, Xinning; Ji, Yang

2017-02-20

Web of Things (WoT) facilitates the discovery and interoperability of Internet of Things (IoT) devices in a cyber-physical system (CPS). Moreover, a uniform knowledge representation of physical resources is quite necessary for further composition, collaboration, and decision-making process in CPS. Though several efforts have integrated semantics with WoT, such as knowledge engineering methods based on semantic sensor networks (SSN), it still could not represent the complex relationships between devices when dynamic composition and collaboration occur, and it totally depends on manual construction of a knowledge base with low scalability. In this paper, to addresses these limitations, we propose the semantic Web of Things (SWoT) framework for CPS (SWoT4CPS). SWoT4CPS provides a hybrid solution with both ontological engineering methods by extending SSN and machine learning methods based on an entity linking (EL) model. To testify to the feasibility and performance, we demonstrate the framework by implementing a temperature anomaly diagnosis and automatic control use case in a building automation system. Evaluation results on the EL method show that linking domain knowledge to DBpedia has a relative high accuracy and the time complexity is at a tolerant level. Advantages and disadvantages of SWoT4CPS with future work are also discussed.

Learning the Semantics of Structured Data Sources

ERIC Educational Resources Information Center

Taheriyan, Mohsen

2015-01-01

Information sources such as relational databases, spreadsheets, XML, JSON, and Web APIs contain a tremendous amount of structured data, however, they rarely provide a semantic model to describe their contents. Semantic models of data sources capture the intended meaning of data sources by mapping them to the concepts and relationships defined by a…

EIIS: An Educational Information Intelligent Search Engine Supported by Semantic Services

ERIC Educational Resources Information Center

Huang, Chang-Qin; Duan, Ru-Lin; Tang, Yong; Zhu, Zhi-Ting; Yan, Yong-Jian; Guo, Yu-Qing

2011-01-01

The semantic web brings a new opportunity for efficient information organization and search. To meet the special requirements of the educational field, this paper proposes an intelligent search engine enabled by educational semantic support service, where three kinds of searches are integrated into Educational Information Intelligent Search (EIIS)…

A Story of a Crashed Plane in US-Mexican border

NASA Astrophysics Data System (ADS)

Bermudez, Luis; Hobona, Gobe; Vretanos, Peter; Peterson, Perry

2013-04-01

A plane has crashed on the US-Mexican border. The search and rescue command center planner needs to find information about the crash site, a mountain, nearby mountains for the establishment of a communications tower, as well as ranches for setting up a local incident center. Events like this one occur all over the world and exchanging information seamlessly is key to save lives and prevent further disasters. This abstract describes an interoperability testbed that applied this scenario using technologies based on Open Geospatial Consortium (OGC) standards. The OGC, which has about 500 members, serves as a global forum for the collaboration of developers and users of spatial data products and services, and to advance the development of international standards for geospatial interoperability. The OGC Interoperability Program conducts international interoperability testbeds, such as the OGC Web Services Phase 9 (OWS-9), that encourages rapid development, testing, validation, demonstration and adoption of open, consensus based standards and best practices. The Cross-Community Interoperability (CCI) thread in OWS-9 advanced the Web Feature Service for Gazetteers (WFS-G) by providing a Single Point of Entry Global Gazetteer (SPEGG), where a user can submit a single query and access global geographic names data across multiple Federal names databases. Currently users must make two queries with differing input parameters against two separate databases to obtain authoritative cross border geographic names data. The gazetteers in this scenario included: GNIS and GNS. GNIS or Geographic Names Information System is managed by USGS. It was first developed in 1964 and contains information about domestic and Antarctic names. GNS or GeoNET Names Server provides the Geographic Names Data Base (GNDB) and it is managed by National Geospatial Intelligence Agency (NGA). GNS has been in service since 1994, and serves names for areas outside the United States and its dependent areas, as well as names for undersea features. The following challenges were advanced: Cascaded WFS-G servers (allowing to query multiple WFSs with a "parent" WFS), implemented query names filters (e.g. fuzzy search, text search), implemented dealing with multilingualism and diacritics, implemented advanced spatial constraints (e.g. search by radial search and nearest neighbor) and semantically mediated feature types (e.g. mountain vs. hill). To enable semantic mediation, a series of semantic mappings were defined between the NGA GNS, USGS GNIS and the Alexandria Digital Library (ADL) Gazetteer. The mappings were encoded in the Web Ontology Language (OWL) to enable them to be used by semantic web technologies. The semantic mappings were then published for ingestion into a semantic mediator that used the mappings to associate location types from one gazetteer with location types in another. The semantic mediator was then able to transform requests on the fly, providing a single point of entry WFS-G to multiple gazetteers. The presentation will provide a live presentation of the work performed, highlight main developments, and discuss future development.

PREDOSE: a semantic web platform for drug abuse epidemiology using social media.

PubMed

Cameron, Delroy; Smith, Gary A; Daniulaityte, Raminta; Sheth, Amit P; Dave, Drashti; Chen, Lu; Anand, Gaurish; Carlson, Robert; Watkins, Kera Z; Falck, Russel

2013-12-01

The role of social media in biomedical knowledge mining, including clinical, medical and healthcare informatics, prescription drug abuse epidemiology and drug pharmacology, has become increasingly significant in recent years. Social media offers opportunities for people to share opinions and experiences freely in online communities, which may contribute information beyond the knowledge of domain professionals. This paper describes the development of a novel semantic web platform called PREDOSE (PREscription Drug abuse Online Surveillance and Epidemiology), which is designed to facilitate the epidemiologic study of prescription (and related) drug abuse practices using social media. PREDOSE uses web forum posts and domain knowledge, modeled in a manually created Drug Abuse Ontology (DAO--pronounced dow), to facilitate the extraction of semantic information from User Generated Content (UGC), through combination of lexical, pattern-based and semantics-based techniques. In a previous study, PREDOSE was used to obtain the datasets from which new knowledge in drug abuse research was derived. Here, we report on various platform enhancements, including an updated DAO, new components for relationship and triple extraction, and tools for content analysis, trend detection and emerging patterns exploration, which enhance the capabilities of the PREDOSE platform. Given these enhancements, PREDOSE is now more equipped to impact drug abuse research by alleviating traditional labor-intensive content analysis tasks. Using custom web crawlers that scrape UGC from publicly available web forums, PREDOSE first automates the collection of web-based social media content for subsequent semantic annotation. The annotation scheme is modeled in the DAO, and includes domain specific knowledge such as prescription (and related) drugs, methods of preparation, side effects, and routes of administration. The DAO is also used to help recognize three types of data, namely: (1) entities, (2) relationships and (3) triples. PREDOSE then uses a combination of lexical and semantic-based techniques to extract entities and relationships from the scraped content, and a top-down approach for triple extraction that uses patterns expressed in the DAO. In addition, PREDOSE uses publicly available lexicons to identify initial sentiment expressions in text, and then a probabilistic optimization algorithm (from related research) to extract the final sentiment expressions. Together, these techniques enable the capture of fine-grained semantic information, which facilitate search, trend analysis and overall content analysis using social media on prescription drug abuse. Moreover, extracted data are also made available to domain experts for the creation of training and test sets for use in evaluation and refinements in information extraction techniques. A recent evaluation of the information extraction techniques applied in the PREDOSE platform indicates 85% precision and 72% recall in entity identification, on a manually created gold standard dataset. In another study, PREDOSE achieved 36% precision in relationship identification and 33% precision in triple extraction, through manual evaluation by domain experts. Given the complexity of the relationship and triple extraction tasks and the abstruse nature of social media texts, we interpret these as favorable initial results. Extracted semantic information is currently in use in an online discovery support system, by prescription drug abuse researchers at the Center for Interventions, Treatment and Addictions Research (CITAR) at Wright State University. A comprehensive platform for entity, relationship, triple and sentiment extraction from such abstruse texts has never been developed for drug abuse research. PREDOSE has already demonstrated the importance of mining social media by providing data from which new findings in drug abuse research were uncovered. Given the recent platform enhancements, including the refined DAO, components for relationship and triple extraction, and tools for content, trend and emerging pattern analysis, it is expected that PREDOSE will play a significant role in advancing drug abuse epidemiology in future. Copyright © 2013 Elsevier Inc. All rights reserved.

Integrating semantic dimension into openEHR archetypes for the management of cerebral palsy electronic medical records.

PubMed

Ellouze, Afef Samet; Bouaziz, Rafik; Ghorbel, Hanen

2016-10-01

Integrating semantic dimension into clinical archetypes is necessary once modeling medical records. First, it enables semantic interoperability and, it offers applying semantic activities on clinical data and provides a higher design quality of Electronic Medical Record (EMR) systems. However, to obtain these advantages, designers need to use archetypes that cover semantic features of clinical concepts involved in their specific applications. In fact, most of archetypes filed within open repositories are expressed in the Archetype Definition Language (ALD) which allows defining only the syntactic structure of clinical concepts weakening semantic activities on the EMR content in the semantic web environment. This paper focuses on the modeling of an EMR prototype for infants affected by Cerebral Palsy (CP), using the dual model approach and integrating semantic web technologies. Such a modeling provides a better delivery of quality of care and ensures semantic interoperability between all involved therapies' information systems. First, data to be documented are identified and collected from the involved therapies. Subsequently, data are analyzed and arranged into archetypes expressed in accordance of ADL. During this step, open archetype repositories are explored, in order to find the suitable archetypes. Then, ADL archetypes are transformed into archetypes expressed in OWL-DL (Ontology Web Language - Description Language). Finally, we construct an ontological source related to these archetypes enabling hence their annotation to facilitate data extraction and providing possibility to exercise semantic activities on such archetypes. Semantic dimension integration into EMR modeled in accordance to the archetype approach. The feasibility of our solution is shown through the development of a prototype, baptized "CP-SMS", which ensures semantic exploitation of CP EMR. This prototype provides the following features: (i) creation of CP EMR instances and their checking by using a knowledge base which we have constructed by interviews with domain experts, (ii) translation of initially CP ADL archetypes into CP OWL-DL archetypes, (iii) creation of an ontological source which we can use to annotate obtained archetypes and (vi) enrichment and supply of the ontological source and integration of semantic relations by providing hence fueling the ontology with new concepts, ensuring consistency and eliminating ambiguity between concepts. The degree of semantic interoperability that could be reached between EMR systems depends strongly on the quality of the used archetypes. Thus, the integration of semantic dimension in archetypes modeling process is crucial. By creating an ontological source and annotating archetypes, we create a supportive platform ensuring semantic interoperability between archetypes-based EMR-systems. Copyright © 2016. Published by Elsevier Inc.

DisGeNET-RDF: harnessing the innovative power of the Semantic Web to explore the genetic basis of diseases.

PubMed

Queralt-Rosinach, Núria; Piñero, Janet; Bravo, Àlex; Sanz, Ferran; Furlong, Laura I

2016-07-15

DisGeNET-RDF makes available knowledge on the genetic basis of human diseases in the Semantic Web. Gene-disease associations (GDAs) and their provenance metadata are published as human-readable and machine-processable web resources. The information on GDAs included in DisGeNET-RDF is interlinked to other biomedical databases to support the development of bioinformatics approaches for translational research through evidence-based exploitation of a rich and fully interconnected linked open data. http://rdf.disgenet.org/ support@disgenet.org. © The Author 2016. Published by Oxford University Press.

Semantic Webbing, Semantic-Pictorial Webbing and Standard Basal Teaching Techniques: A Comparison of Three Strategies To Enhance Learning and Memory of a Reading Comprehension Task in the Fourth Grade Classroom.

ERIC Educational Resources Information Center

McCarthy-Tucker, Sherri

A study analyzed the relative effectiveness of three teaching strategies for enhancing vocabulary and reading comprehension. Sixty-eight students in three fourth-grade classrooms in a suburban southwestern public school were presented with a vocabulary lesson on weather from the reading text according to one of the following strategies: (1) basal…

Semantic labeling of digital photos by classification

NASA Astrophysics Data System (ADS)

Ciocca, Gianluigi; Cusano, Claudio; Schettini, Raimondo; Brambilla, Carla

2003-01-01

The paper addresses the problem of annotating photographs with broad semantic labels. To cope with the great variety of photos available on the WEB we have designed a hierarchical classification strategy which first classifies images as pornographic or not-pornographic. Not-pornographic images are then classified as indoor, outdoor, or close-up. On a database of over 9000 images, mostly downloaded from the web, our method achieves an average accuracy of close to 90%.

Toward Webscale, Rule-Based Inference on the Semantic Web Via Data Parallelism

DTIC Science & Technology

2013-02-01

Another work distinct from its peers is the work on approximate reasoning by Rudolph et al. [34] in which multiple inference sys- tems were combined not...Workshop Scalable Semantic Web Knowledge Base Systems, 2010, pp. 17–31. [34] S. Rudolph , T. Tserendorj, and P. Hitzler, “What is approximate reasoning...2013] [55] M. Duerst and M. Suignard. (2005, Jan .). RFC 3987 – internationalized resource identifiers (IRIs). IETF. [Online]. Available: http

Mining Genotype-Phenotype Associations from Public Knowledge Sources via Semantic Web Querying.

PubMed

Kiefer, Richard C; Freimuth, Robert R; Chute, Christopher G; Pathak, Jyotishman

2013-01-01

Gene Wiki Plus (GeneWiki+) and the Online Mendelian Inheritance in Man (OMIM) are publicly available resources for sharing information about disease-gene and gene-SNP associations in humans. While immensely useful to the scientific community, both resources are manually curated, thereby making the data entry and publication process time-consuming, and to some degree, error-prone. To this end, this study investigates Semantic Web technologies to validate existing and potentially discover new genotype-phenotype associations in GWP and OMIM. In particular, we demonstrate the applicability of SPARQL queries for identifying associations not explicitly stated for commonly occurring chronic diseases in GWP and OMIM, and report our preliminary findings for coverage, completeness, and validity of the associations. Our results highlight the benefits of Semantic Web querying technology to validate existing disease-gene associations as well as identify novel associations although further evaluation and analysis is required before such information can be applied and used effectively.

Semantic enrichment of medical forms - semi-automated coding of ODM-elements via web services.

PubMed

Breil, Bernhard; Watermann, Andreas; Haas, Peter; Dziuballe, Philipp; Dugas, Martin

2012-01-01

Semantic interoperability is an unsolved problem which occurs while working with medical forms from different information systems or institutions. Standards like ODM or CDA assure structural homogenization but in order to compare elements from different data models it is necessary to use semantic concepts and codes on an item level of those structures. We developed and implemented a web-based tool which enables a domain expert to perform semi-automated coding of ODM-files. For each item it is possible to inquire web services which result in unique concept codes without leaving the context of the document. Although it was not feasible to perform a totally automated coding we have implemented a dialog based method to perform an efficient coding of all data elements in the context of the whole document. The proportion of codable items was comparable to results from previous studies.

Towards Semantic Web Services on Large, Multi-Dimensional Coverages

NASA Astrophysics Data System (ADS)

Baumann, P.

2009-04-01

Observed and simulated data in the Earth Sciences often come as coverages, the general term for space-time varying phenomena as set forth by standardization bodies like the Open GeoSpatial Consortium (OGC) and ISO. Among such data are 1-d time series, 2-D surface data, 3-D surface data time series as well as x/y/z geophysical and oceanographic data, and 4-D metocean simulation results. With increasing dimensionality the data sizes grow exponentially, up to Petabyte object sizes. Open standards for exploiting coverage archives over the Web are available to a varying extent. The OGC Web Coverage Service (WCS) standard defines basic extraction operations: spatio-temporal and band subsetting, scaling, reprojection, and data format encoding of the result - a simple interoperable interface for coverage access. More processing functionality is available with products like Matlab, Grid-type interfaces, and the OGC Web Processing Service (WPS). However, these often lack properties known as advantageous from databases: declarativeness (describe results rather than the algorithms), safe in evaluation (no request can keep a server busy infinitely), and optimizable (enable the server to rearrange the request so as to produce the same result faster). WPS defines a geo-enabled SOAP interface for remote procedure calls. This allows to webify any program, but does not allow for semantic interoperability: a function is identified only by its function name and parameters while the semantics is encoded in the (only human readable) title and abstract. Hence, another desirable property is missing, namely an explicit semantics which allows for machine-machine communication and reasoning a la Semantic Web. The OGC Web Coverage Processing Service (WCPS) language, which has been adopted as an international standard by OGC in December 2008, defines a flexible interface for the navigation, extraction, and ad-hoc analysis of large, multi-dimensional raster coverages. It is abstract in that it does not anticipate any particular protocol. One such protocol is given by the OGC Web Coverage Service (WCS) Processing Extension standard which ties WCPS into WCS. Another protocol which makes WCPS an OGC Web Processing Service (WPS) Profile is under preparation. Thereby, WCPS bridges WCS and WPS. The conceptual model of WCPS relies on the coverage model of WCS, which in turn is based on ISO 19123. WCS currently addresses raster-type coverages where a coverage is seen as a function mapping points from a spatio-temporal extent (its domain) into values of some cell type (its range). A retrievable coverage has an identifier associated, further the CRSs supported and, for each range field (aka band, channel), the interpolation methods applicable. The WCPS language offers access to one or several such coverages via a functional, side-effect free language. The following example, which derives the NDVI (Normalized Difference Vegetation Index) from given coverages C1, C2, and C3 within the regions identified by the binary mask R, illustrates the language concept: for c in ( C1, C2, C3 ), r in ( R ) return encode( (char) (c.nir - c.red) / (c.nir + c.red), H˜DF-EOS\\~ ) The result is a list of three HDF-EOS encoded images containing masked NDVI values. Note that the same request can operate on coverages of any dimensionality. The expressive power of WCPS includes statistics, image, and signal processing up to recursion, to maintain safe evaluation. As both syntax and semantics of any WCPS expression is well known the language is Semantic Web ready: clients can construct WCPS requests on the fly, servers can optimize such requests (this has been investigated extensively with the rasdaman raster database system) and automatically distribute them for processing in a WCPS-enabled computing cloud. The WCPS Reference Implementation is being finalized now that the standard is stable; it will be released in open source once ready. Among the future tasks is to extend WCPS to general meshes, in synchronization with the WCS standard. In this talk WCPS is presented in the context of OGC standardization. The author is co-chair of OGC's WCS Working Group (WG) and Coverages WG.

Algorithms and semantic infrastructure for mutation impact extraction and grounding.

PubMed

Laurila, Jonas B; Naderi, Nona; Witte, René; Riazanov, Alexandre; Kouznetsov, Alexandre; Baker, Christopher J O

2010-12-02

Mutation impact extraction is a hitherto unaccomplished task in state of the art mutation extraction systems. Protein mutations and their impacts on protein properties are hidden in scientific literature, making them poorly accessible for protein engineers and inaccessible for phenotype-prediction systems that currently depend on manually curated genomic variation databases. We present the first rule-based approach for the extraction of mutation impacts on protein properties, categorizing their directionality as positive, negative or neutral. Furthermore protein and mutation mentions are grounded to their respective UniProtKB IDs and selected protein properties, namely protein functions to concepts found in the Gene Ontology. The extracted entities are populated to an OWL-DL Mutation Impact ontology facilitating complex querying for mutation impacts using SPARQL. We illustrate retrieval of proteins and mutant sequences for a given direction of impact on specific protein properties. Moreover we provide programmatic access to the data through semantic web services using the SADI (Semantic Automated Discovery and Integration) framework. We address the problem of access to legacy mutation data in unstructured form through the creation of novel mutation impact extraction methods which are evaluated on a corpus of full-text articles on haloalkane dehalogenases, tagged by domain experts. Our approaches show state of the art levels of precision and recall for Mutation Grounding and respectable level of precision but lower recall for the task of Mutant-Impact relation extraction. The system is deployed using text mining and semantic web technologies with the goal of publishing to a broad spectrum of consumers.

Knowledge-based personalized search engine for the Web-based Human Musculoskeletal System Resources (HMSR) in biomechanics.

PubMed

Dao, Tien Tuan; Hoang, Tuan Nha; Ta, Xuan Hien; Tho, Marie Christine Ho Ba

2013-02-01

Human musculoskeletal system resources of the human body are valuable for the learning and medical purposes. Internet-based information from conventional search engines such as Google or Yahoo cannot response to the need of useful, accurate, reliable and good-quality human musculoskeletal resources related to medical processes, pathological knowledge and practical expertise. In this present work, an advanced knowledge-based personalized search engine was developed. Our search engine was based on a client-server multi-layer multi-agent architecture and the principle of semantic web services to acquire dynamically accurate and reliable HMSR information by a semantic processing and visualization approach. A security-enhanced mechanism was applied to protect the medical information. A multi-agent crawler was implemented to develop a content-based database of HMSR information. A new semantic-based PageRank score with related mathematical formulas were also defined and implemented. As the results, semantic web service descriptions were presented in OWL, WSDL and OWL-S formats. Operational scenarios with related web-based interfaces for personal computers and mobile devices were presented and analyzed. Functional comparison between our knowledge-based search engine, a conventional search engine and a semantic search engine showed the originality and the robustness of our knowledge-based personalized search engine. In fact, our knowledge-based personalized search engine allows different users such as orthopedic patient and experts or healthcare system managers or medical students to access remotely into useful, accurate, reliable and good-quality HMSR information for their learning and medical purposes. Copyright © 2012 Elsevier Inc. All rights reserved.

E-Learning 3.0 = E-Learning 2.0 + Web 3.0?

ERIC Educational Resources Information Center

Hussain, Fehmida

2012-01-01

Web 3.0, termed as the semantic web or the web of data is the transformed version of Web 2.0 with technologies and functionalities such as intelligent collaborative filtering, cloud computing, big data, linked data, openness, interoperability and smart mobility. If Web 2.0 is about social networking and mass collaboration between the creator and…

A novel visualization model for web search results.

PubMed

Nguyen, Tien N; Zhang, Jin

2006-01-01

This paper presents an interactive visualization system, named WebSearchViz, for visualizing the Web search results and acilitating users' navigation and exploration. The metaphor in our model is the solar system with its planets and asteroids revolving around the sun. Location, color, movement, and spatial distance of objects in the visual space are used to represent the semantic relationships between a query and relevant Web pages. Especially, the movement of objects and their speeds add a new dimension to the visual space, illustrating the degree of relevance among a query and Web search results in the context of users' subjects of interest. By interacting with the visual space, users are able to observe the semantic relevance between a query and a resulting Web page with respect to their subjects of interest, context information, or concern. Users' subjects of interest can be dynamically changed, redefined, added, or deleted from the visual space.

Can Social Semantic Web Techniques Foster Collaborative Curriculum Mapping In Medicine?

PubMed Central

Finsterer, Sonja; Cremer, Jan; Schenkat, Hennig

2013-01-01

Background Curriculum mapping, which is aimed at the systematic realignment of the planned, taught, and learned curriculum, is considered a challenging and ongoing effort in medical education. Second-generation curriculum managing systems foster knowledge management processes including curriculum mapping in order to give comprehensive support to learners, teachers, and administrators. The large quantity of custom-built software in this field indicates a shortcoming of available IT tools and standards. Objective The project reported here aims at the systematic adoption of techniques and standards of the Social Semantic Web to implement collaborative curriculum mapping for a complete medical model curriculum. Methods A semantic MediaWiki (SMW)-based Web application has been introduced as a platform for the elicitation and revision process of the Aachen Catalogue of Learning Objectives (ACLO). The semantic wiki uses a domain model of the curricular context and offers structured (form-based) data entry, multiple views, structured querying, semantic indexing, and commenting for learning objectives (“LOs”). Semantic indexing of learning objectives relies on both a controlled vocabulary of international medical classifications (ICD, MeSH) and a folksonomy maintained by the users. An additional module supporting the global checking of consistency complements the semantic wiki. Statements of the Object Constraint Language define the consistency criteria. We evaluated the application by a scenario-based formative usability study, where the participants solved tasks in the (fictional) context of 7 typical situations and answered a questionnaire containing Likert-scaled items and free-text questions. Results At present, ACLO contains roughly 5350 operational (ie, specific and measurable) objectives acquired during the last 25 months. The wiki-based user interface uses 13 online forms for data entry and 4 online forms for flexible searches of LOs, and all the forms are accessible by standard Web browsers. The formative usability study yielded positive results (median rating of 2 (“good”) in all 7 general usability items) and produced valuable qualitative feedback, especially concerning navigation and comprehensibility. Although not asked to, the participants (n=5) detected critical aspects of the curriculum (similar learning objectives addressed repeatedly and missing objectives), thus proving the system’s ability to support curriculum revision. Conclusions The SMW-based approach enabled an agile implementation of computer-supported knowledge management. The approach, based on standard Social Semantic Web formats and technology, represents a feasible and effectively applicable compromise between answering to the individual requirements of curriculum management at a particular medical school and using proprietary systems. PMID:23948519

Designing Collaborative E-Learning Environments Based upon Semantic Wiki: From Design Models to Application Scenarios

ERIC Educational Resources Information Center

Li, Yanyan; Dong, Mingkai; Huang, Ronghuai

2011-01-01

The knowledge society requires life-long learning and flexible learning environment that enables fast, just-in-time and relevant learning, aiding the development of communities of knowledge, linking learners and practitioners with experts. Based upon semantic wiki, a combination of wiki and Semantic Web technology, this paper designs and develops…

Automatically exposing OpenLifeData via SADI semantic Web Services.

PubMed

González, Alejandro Rodríguez; Callahan, Alison; Cruz-Toledo, José; Garcia, Adrian; Egaña Aranguren, Mikel; Dumontier, Michel; Wilkinson, Mark D

2014-01-01

Two distinct trends are emerging with respect to how data is shared, collected, and analyzed within the bioinformatics community. First, Linked Data, exposed as SPARQL endpoints, promises to make data easier to collect and integrate by moving towards the harmonization of data syntax, descriptive vocabularies, and identifiers, as well as providing a standardized mechanism for data access. Second, Web Services, often linked together into workflows, normalize data access and create transparent, reproducible scientific methodologies that can, in principle, be re-used and customized to suit new scientific questions. Constructing queries that traverse semantically-rich Linked Data requires substantial expertise, yet traditional RESTful or SOAP Web Services cannot adequately describe the content of a SPARQL endpoint. We propose that content-driven Semantic Web Services can enable facile discovery of Linked Data, independent of their location. We use a well-curated Linked Dataset - OpenLifeData - and utilize its descriptive metadata to automatically configure a series of more than 22,000 Semantic Web Services that expose all of its content via the SADI set of design principles. The OpenLifeData SADI services are discoverable via queries to the SHARE registry and easy to integrate into new or existing bioinformatics workflows and analytical pipelines. We demonstrate the utility of this system through comparison of Web Service-mediated data access with traditional SPARQL, and note that this approach not only simplifies data retrieval, but simultaneously provides protection against resource-intensive queries. We show, through a variety of different clients and examples of varying complexity, that data from the myriad OpenLifeData can be recovered without any need for prior-knowledge of the content or structure of the SPARQL endpoints. We also demonstrate that, via clients such as SHARE, the complexity of federated SPARQL queries is dramatically reduced.

Seahawk: moving beyond HTML in Web-based bioinformatics analysis.

PubMed

Gordon, Paul M K; Sensen, Christoph W

2007-06-18

Traditional HTML interfaces for input to and output from Bioinformatics analysis on the Web are highly variable in style, content and data formats. Combining multiple analyses can therefore be an onerous task for biologists. Semantic Web Services allow automated discovery of conceptual links between remote data analysis servers. A shared data ontology and service discovery/execution framework is particularly attractive in Bioinformatics, where data and services are often both disparate and distributed. Instead of biologists copying, pasting and reformatting data between various Web sites, Semantic Web Service protocols such as MOBY-S hold out the promise of seamlessly integrating multi-step analysis. We have developed a program (Seahawk) that allows biologists to intuitively and seamlessly chain together Web Services using a data-centric, rather than the customary service-centric approach. The approach is illustrated with a ferredoxin mutation analysis. Seahawk concentrates on lowering entry barriers for biologists: no prior knowledge of the data ontology, or relevant services is required. In stark contrast to other MOBY-S clients, in Seahawk users simply load Web pages and text files they already work with. Underlying the familiar Web-browser interaction is an XML data engine based on extensible XSLT style sheets, regular expressions, and XPath statements which import existing user data into the MOBY-S format. As an easily accessible applet, Seahawk moves beyond standard Web browser interaction, providing mechanisms for the biologist to concentrate on the analytical task rather than on the technical details of data formats and Web forms. As the MOBY-S protocol nears a 1.0 specification, we expect more biologists to adopt these new semantic-oriented ways of doing Web-based analysis, which empower them to do more complicated, ad hoc analysis workflow creation without the assistance of a programmer.

Seahawk: moving beyond HTML in Web-based bioinformatics analysis

PubMed Central

Gordon, Paul MK; Sensen, Christoph W

2007-01-01

Background Traditional HTML interfaces for input to and output from Bioinformatics analysis on the Web are highly variable in style, content and data formats. Combining multiple analyses can therfore be an onerous task for biologists. Semantic Web Services allow automated discovery of conceptual links between remote data analysis servers. A shared data ontology and service discovery/execution framework is particularly attractive in Bioinformatics, where data and services are often both disparate and distributed. Instead of biologists copying, pasting and reformatting data between various Web sites, Semantic Web Service protocols such as MOBY-S hold out the promise of seamlessly integrating multi-step analysis. Results We have developed a program (Seahawk) that allows biologists to intuitively and seamlessly chain together Web Services using a data-centric, rather than the customary service-centric approach. The approach is illustrated with a ferredoxin mutation analysis. Seahawk concentrates on lowering entry barriers for biologists: no prior knowledge of the data ontology, or relevant services is required. In stark contrast to other MOBY-S clients, in Seahawk users simply load Web pages and text files they already work with. Underlying the familiar Web-browser interaction is an XML data engine based on extensible XSLT style sheets, regular expressions, and XPath statements which import existing user data into the MOBY-S format. Conclusion As an easily accessible applet, Seahawk moves beyond standard Web browser interaction, providing mechanisms for the biologist to concentrate on the analytical task rather than on the technical details of data formats and Web forms. As the MOBY-S protocol nears a 1.0 specification, we expect more biologists to adopt these new semantic-oriented ways of doing Web-based analysis, which empower them to do more complicated, ad hoc analysis workflow creation without the assistance of a programmer. PMID:17577405

BioSWR – Semantic Web Services Registry for Bioinformatics

PubMed Central

Repchevsky, Dmitry; Gelpi, Josep Ll.

2014-01-01

Despite of the variety of available Web services registries specially aimed at Life Sciences, their scope is usually restricted to a limited set of well-defined types of services. While dedicated registries are generally tied to a particular format, general-purpose ones are more adherent to standards and usually rely on Web Service Definition Language (WSDL). Although WSDL is quite flexible to support common Web services types, its lack of semantic expressiveness led to various initiatives to describe Web services via ontology languages. Nevertheless, WSDL 2.0 descriptions gained a standard representation based on Web Ontology Language (OWL). BioSWR is a novel Web services registry that provides standard Resource Description Framework (RDF) based Web services descriptions along with the traditional WSDL based ones. The registry provides Web-based interface for Web services registration, querying and annotation, and is also accessible programmatically via Representational State Transfer (REST) API or using a SPARQL Protocol and RDF Query Language. BioSWR server is located at http://inb.bsc.es/BioSWR/and its code is available at https://sourceforge.net/projects/bioswr/under the LGPL license. PMID:25233118

BioSWR--semantic web services registry for bioinformatics.

PubMed

Repchevsky, Dmitry; Gelpi, Josep Ll

2014-01-01

Despite of the variety of available Web services registries specially aimed at Life Sciences, their scope is usually restricted to a limited set of well-defined types of services. While dedicated registries are generally tied to a particular format, general-purpose ones are more adherent to standards and usually rely on Web Service Definition Language (WSDL). Although WSDL is quite flexible to support common Web services types, its lack of semantic expressiveness led to various initiatives to describe Web services via ontology languages. Nevertheless, WSDL 2.0 descriptions gained a standard representation based on Web Ontology Language (OWL). BioSWR is a novel Web services registry that provides standard Resource Description Framework (RDF) based Web services descriptions along with the traditional WSDL based ones. The registry provides Web-based interface for Web services registration, querying and annotation, and is also accessible programmatically via Representational State Transfer (REST) API or using a SPARQL Protocol and RDF Query Language. BioSWR server is located at http://inb.bsc.es/BioSWR/and its code is available at https://sourceforge.net/projects/bioswr/under the LGPL license.

Linking Disparate Datasets of the Earth Sciences with the SemantEco Annotator

NASA Astrophysics Data System (ADS)

Seyed, P.; Chastain, K.; McGuinness, D. L.

2013-12-01

Use of Semantic Web technologies for data management in the Earth sciences (and beyond) has great potential but is still in its early stages, since the challenges of translating data into a more explicit or semantic form for immediate use within applications has not been fully addressed. In this abstract we help address this challenge by introducing the SemantEco Annotator, which enables anyone, regardless of expertise, to semantically annotate tabular Earth Science data and translate it into linked data format, while applying the logic inherent in community-standard vocabularies to guide the process. The Annotator was conceived under a desire to unify dataset content from a variety of sources under common vocabularies, for use in semantically-enabled web applications. Our current use case employs linked data generated by the Annotator for use in the SemantEco environment, which utilizes semantics to help users explore, search, and visualize water or air quality measurement and species occurrence data through a map-based interface. The generated data can also be used immediately to facilitate discovery and search capabilities within 'big data' environments. The Annotator provides a method for taking information about a dataset, that may only be known to its maintainers, and making it explicit, in a uniform and machine-readable fashion, such that a person or information system can more easily interpret the underlying structure and meaning. Its primary mechanism is to enable a user to formally describe how columns of a tabular dataset relate and/or describe entities. For example, if a user identifies columns for latitude and longitude coordinates, we can infer the data refers to a point that can be plotted on a map. Further, it can be made explicit that measurements of 'nitrate' and 'NO3-' are of the same entity through vocabulary assignments, thus more easily utilizing data sets that use different nomenclatures. The Annotator provides an extensive and searchable library of vocabularies to assist the user in locating terms to describe observed entities, their properties, and relationships. The Annotator leverages vocabulary definitions of these concepts to guide the user in describing data in a logically consistent manner. The vocabularies made available through the Annotator are open, as is the Annotator itself. We have taken a step towards making semantic annotation/translation of data more accessible. Our vision for the Annotator is as a tool that can be integrated into a semantic data 'workbench' environment, which would allow semantic annotation of a variety of data formats, using standard vocabularies. These vocabularies involved enable search for similar datasets, and integration with any semantically-enabled applications for analysis and visualization.

On Propagating Interpersonal Trust in Social Networks

NASA Astrophysics Data System (ADS)

Ziegler, Cai-Nicolas

The age of information glut has fostered the proliferation of data and documents on the Web, created by man and machine alike. Hence, there is an enormous wealth of minable knowledge that is yet to be extracted, in particular, on the Semantic Web. However, besides understanding information stated by subjects, knowing about their credibility becomes equally crucial. Hence, trust and trust metrics, conceived as computational means to evaluate trust relationships between individuals, come into play. Our major contribution to Semantic Web trust management through this work is twofold. First, we introduce a classification scheme for trust metrics along various axes and discuss advantages and drawbacks of existing approaches for Semantic Web scenarios. Hereby, we devise an advocacy for local group trust metrics, guiding us to the second part, which presents Appleseed, our novel proposal for local group trust computation. Compelling in its simplicity, Appleseed borrows many ideas from spreading activation models in psychology and relates their concepts to trust evaluation in an intuitive fashion. Moreover, we provide extensions for the Appleseed nucleus that make our trust metric handle distrust statements.

Vigi4Med Scraper: A Framework for Web Forum Structured Data Extraction and Semantic Representation

PubMed Central

Audeh, Bissan; Beigbeder, Michel; Zimmermann, Antoine; Jaillon, Philippe; Bousquet, Cédric

2017-01-01

The extraction of information from social media is an essential yet complicated step for data analysis in multiple domains. In this paper, we present Vigi4Med Scraper, a generic open source framework for extracting structured data from web forums. Our framework is highly configurable; using a configuration file, the user can freely choose the data to extract from any web forum. The extracted data are anonymized and represented in a semantic structure using Resource Description Framework (RDF) graphs. This representation enables efficient manipulation by data analysis algorithms and allows the collected data to be directly linked to any existing semantic resource. To avoid server overload, an integrated proxy with caching functionality imposes a minimal delay between sequential requests. Vigi4Med Scraper represents the first step of Vigi4Med, a project to detect adverse drug reactions (ADRs) from social networks founded by the French drug safety agency Agence Nationale de Sécurité du Médicament (ANSM). Vigi4Med Scraper has successfully extracted greater than 200 gigabytes of data from the web forums of over 20 different websites. PMID:28122056

Research of three level match method about semantic web service based on ontology

NASA Astrophysics Data System (ADS)

Xiao, Jie; Cai, Fang

2011-10-01

An important step of Web service Application is the discovery of useful services. Keywords are used in service discovery in traditional technology like UDDI and WSDL, with the disadvantage of user intervention, lack of semantic description and low accuracy. To cope with these problems, OWL-S is introduced and extended with QoS attributes to describe the attribute and functions of Web Services. A three-level service matching algorithm based on ontology and QOS in proposed in this paper. Our algorithm can match web service by utilizing the service profile, QoS parameters together with input and output of the service. Simulation results shows that it greatly enhanced the speed of service matching while high accuracy is also guaranteed.

ResearchEHR: use of semantic web technologies and archetypes for the description of EHRs.

PubMed

Robles, Montserrat; Fernández-Breis, Jesualdo Tomás; Maldonado, Jose A; Moner, David; Martínez-Costa, Catalina; Bosca, Diego; Menárguez-Tortosa, Marcos

2010-01-01

In this paper, we present the ResearchEHR project. It focuses on the usability of Electronic Health Record (EHR) sources and EHR standards for building advanced clinical systems. The aim is to support healthcare professional, institutions and authorities by providing a set of generic methods and tools for the capture, standardization, integration, description and dissemination of health related information. ResearchEHR combines several tools to manage EHR at two different levels. The internal level that deals with the normalization and semantic upgrading of exiting EHR by using archetypes and the external level that uses Semantic Web technologies to specify clinical archetypes for advanced EHR architectures and systems.

S3DB core: a framework for RDF generation and management in bioinformatics infrastructures

PubMed Central

2010-01-01

Background Biomedical research is set to greatly benefit from the use of semantic web technologies in the design of computational infrastructure. However, beyond well defined research initiatives, substantial issues of data heterogeneity, source distribution, and privacy currently stand in the way towards the personalization of Medicine. Results A computational framework for bioinformatic infrastructure was designed to deal with the heterogeneous data sources and the sensitive mixture of public and private data that characterizes the biomedical domain. This framework consists of a logical model build with semantic web tools, coupled with a Markov process that propagates user operator states. An accompanying open source prototype was developed to meet a series of applications that range from collaborative multi-institution data acquisition efforts to data analysis applications that need to quickly traverse complex data structures. This report describes the two abstractions underlying the S3DB-based infrastructure, logical and numerical, and discusses its generality beyond the immediate confines of existing implementations. Conclusions The emergence of the "web as a computer" requires a formal model for the different functionalities involved in reading and writing to it. The S3DB core model proposed was found to address the design criteria of biomedical computational infrastructure, such as those supporting large scale multi-investigator research, clinical trials, and molecular epidemiology. PMID:20646315

Semantic Web repositories for genomics data using the eXframe platform

PubMed Central

2014-01-01

Background With the advent of inexpensive assay technologies, there has been an unprecedented growth in genomics data as well as the number of databases in which it is stored. In these databases, sample annotation using ontologies and controlled vocabularies is becoming more common. However, the annotation is rarely available as Linked Data, in a machine-readable format, or for standardized queries using SPARQL. This makes large-scale reuse, or integration with other knowledge bases very difficult. Methods To address this challenge, we have developed the second generation of our eXframe platform, a reusable framework for creating online repositories of genomics experiments. This second generation model now publishes Semantic Web data. To accomplish this, we created an experiment model that covers provenance, citations, external links, assays, biomaterials used in the experiment, and the data collected during the process. The elements of our model are mapped to classes and properties from various established biomedical ontologies. Resource Description Framework (RDF) data is automatically produced using these mappings and indexed in an RDF store with a built-in Sparql Protocol and RDF Query Language (SPARQL) endpoint. Conclusions Using the open-source eXframe software, institutions and laboratories can create Semantic Web repositories of their experiments, integrate it with heterogeneous resources and make it interoperable with the vast Semantic Web of biomedical knowledge. PMID:25093072

A New Approach for Semantic Web Matching

NASA Astrophysics Data System (ADS)

Zamanifar, Kamran; Heidary, Golsa; Nematbakhsh, Naser; Mardukhi, Farhad

In this work we propose a new approach for semantic web matching to improve the performance of Web Service replacement. Because in automatic systems we should ensure the self-healing, self-configuration, self-optimization and self-management, all services should be always available and if one of them crashes, it should be replaced with the most similar one. Candidate services are advertised in Universal Description, Discovery and Integration (UDDI) all in Web Ontology Language (OWL). By the help of bipartite graph, we did the matching between the crashed service and a Candidate one. Then we chose the best service, which had the maximum rate of matching. In fact we compare two services' functionalities and capabilities to see how much they match. We found that the best way for matching two web services, is comparing the functionalities of them.

Practical solutions to implementing "Born Semantic" data systems

NASA Astrophysics Data System (ADS)

Leadbetter, A.; Buck, J. J. H.; Stacey, P.

2015-12-01

The concept of data being "Born Semantic" has been proposed in recent years as a Semantic Web analogue to the idea of data being "born digital"[1], [2]. Within the "Born Semantic" concept, data are captured digitally and at a point close to the time of creation are annotated with markup terms from semantic web resources (controlled vocabularies, thesauri or ontologies). This allows heterogeneous data to be more easily ingested and amalgamated in near real-time due to the standards compliant annotation of the data. In taking the "Born Semantic" proposal from concept to operation, a number of difficulties have been encountered. For example, although there are recognised methods such as Header, Dictionary, Triples [3] for the compression, publication and dissemination of large volumes of triples these systems are not practical to deploy in the field on low-powered (both electrically and computationally) devices. Similarly, it is not practical for instruments to output fully formed semantically annotated data files if they are designed to be plugged into a modular system and the data to be centrally logged in the field as is the case on Argo floats and oceanographic gliders where internal bandwidth becomes an issue [2]. In light of these issues, this presentation will concentrate on pragmatic solutions being developed to the problem of generating Linked Data in near real-time systems. Specific examples from the European Commission SenseOCEAN project where Linked Data systems are being developed for autonomous underwater platforms, and from work being undertaken in the streaming of data from the Irish Galway Bay Cable Observatory initiative will be highlighted. Further, developments of a set of tools for the LogStash-ElasticSearch software ecosystem to allow the storing and retrieval of Linked Data will be introduced. References[1] A. Leadbetter & J. Fredericks, We have "born digital" - now what about "born semantic"?, European Geophysical Union General Assembly, 2014.[2] J. Buck & A. Leadbetter, Born semantic: linking data from sensors to users and balancing hardware limitations with data standards, European Geophysical Union General Assembly, 2015.[3] J. Fernandez et al., Binary RDF Representation for Publication and Exchange (HDT), Web Semantics 19:22-41, 2013.

The Digital electronic Guideline Library (DeGeL): a hybrid framework for representation and use of clinical guidelines.

PubMed

Shahar, Yuval; Young, Ohad; Shalom, Erez; Mayaffit, Alon; Moskovitch, Robert; Hessing, Alon; Galperin, Maya

2004-01-01

We propose to present a poster (and potentially also a demonstration of the implemented system) summarizing the current state of our work on a hybrid, multiple-format representation of clinical guidelines that facilitates conversion of guidelines from free text to a formal representation. We describe a distributed Web-based architecture (DeGeL) and a set of tools using the hybrid representation. The tools enable performing tasks such as guideline specification, semantic markup, search, retrieval, visualization, eligibility determination, runtime application and retrospective quality assessment. The representation includes four parallel formats: Free text (one or more original sources); semistructured text (labeled by the target guideline-ontology semantic labels); semiformal text (which includes some control specification); and a formal, machine-executable representation. The specification, indexing, search, retrieval, and browsing tools are essentially independent of the ontology chosen for guideline representation, but editing the semi-formal and formal formats requires ontology-specific tools, which we have developed in the case of the Asbru guideline-specification language. The four formats support increasingly sophisticated computational tasks. The hybrid guidelines are stored in a Web-based library. All tools, such as for runtime guideline application or retrospective quality assessment, are designed to operate on all representations. We demonstrate the hybrid framework by providing examples from the semantic markup and search tools.

Modeling and validating HL7 FHIR profiles using semantic web Shape Expressions (ShEx).

PubMed

Solbrig, Harold R; Prud'hommeaux, Eric; Grieve, Grahame; McKenzie, Lloyd; Mandel, Joshua C; Sharma, Deepak K; Jiang, Guoqian

2017-03-01

HL7 Fast Healthcare Interoperability Resources (FHIR) is an emerging open standard for the exchange of electronic healthcare information. FHIR resources are defined in a specialized modeling language. FHIR instances can currently be represented in either XML or JSON. The FHIR and Semantic Web communities are developing a third FHIR instance representation format in Resource Description Framework (RDF). Shape Expressions (ShEx), a formal RDF data constraint language, is a candidate for describing and validating the FHIR RDF representation. Create a FHIR to ShEx model transformation and assess its ability to describe and validate FHIR RDF data. We created the methods and tools that generate the ShEx schemas modeling the FHIR to RDF specification being developed by HL7 ITS/W3C RDF Task Force, and evaluated the applicability of ShEx in the description and validation of FHIR to RDF transformations. The ShEx models contributed significantly to workgroup consensus. Algorithmic transformations from the FHIR model to ShEx schemas and FHIR example data to RDF transformations were incorporated into the FHIR build process. ShEx schemas representing 109 FHIR resources were used to validate 511 FHIR RDF data examples from the Standards for Trial Use (STU 3) Ballot version. We were able to uncover unresolved issues in the FHIR to RDF specification and detect 10 types of errors and root causes in the actual implementation. The FHIR ShEx representations have been included in the official FHIR web pages for the STU 3 Ballot version since September 2016. ShEx can be used to define and validate the syntax of a FHIR resource, which is complementary to the use of RDF Schema (RDFS) and Web Ontology Language (OWL) for semantic validation. ShEx proved useful for describing a standard model of FHIR RDF data. The combination of a formal model and a succinct format enabled comprehensive review and automated validation. Copyright © 2017 Elsevier Inc. All rights reserved.

Semantic Body Browser: graphical exploration of an organism and spatially resolved expression data visualization.

PubMed

Lekschas, Fritz; Stachelscheid, Harald; Seltmann, Stefanie; Kurtz, Andreas

2015-03-01

Advancing technologies generate large amounts of molecular and phenotypic data on cells, tissues and organisms, leading to an ever-growing detail and complexity while information retrieval and analysis becomes increasingly time-consuming. The Semantic Body Browser is a web application for intuitively exploring the body of an organism from the organ to the subcellular level and visualising expression profiles by means of semantically annotated anatomical illustrations. It is used to comprehend biological and medical data related to the different body structures while relying on the strong pattern recognition capabilities of human users. The Semantic Body Browser is a JavaScript web application that is freely available at http://sbb.cellfinder.org. The source code is provided on https://github.com/flekschas/sbb. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Semantically Enriching the Search System of a Music Digital Library

NASA Astrophysics Data System (ADS)

de Juan, Paloma; Iglesias, Carlos

Traditional search systems are usually based on keywords, a very simple and convenient mechanism to express a need for information. This is the most popular way of searching the Web, although it is not always an easy task to accurately summarize a natural language query in a few keywords. Working with keywords means losing the context, which is the only thing that can help us deal with ambiguity. This is the biggest problem of keyword-based systems. Semantic Web technologies seem a perfect solution to this problem, since they make it possible to represent the semantics of a given domain. In this chapter, we present three projects, Harmos, Semusici and Cantiga, whose aim is to provide access to a music digital library. We will describe two search systems, a traditional one and a semantic one, developed in the context of these projects and compare them in terms of usability and effectiveness.

Semantic interpretation of search engine resultant

NASA Astrophysics Data System (ADS)

Nasution, M. K. M.

2018-01-01

In semantic, logical language can be interpreted in various forms, but the certainty of meaning is included in the uncertainty, which directly always influences the role of technology. One results of this uncertainty applies to search engines as user interfaces with information spaces such as the Web. Therefore, the behaviour of search engine results should be interpreted with certainty through semantic formulation as interpretation. Behaviour formulation shows there are various interpretations that can be done semantically either temporary, inclusion, or repeat.

Semantically enabled and statistically supported biological hypothesis testing with tissue microarray databases

PubMed Central

2011-01-01

Background Although many biological databases are applying semantic web technologies, meaningful biological hypothesis testing cannot be easily achieved. Database-driven high throughput genomic hypothesis testing requires both of the capabilities of obtaining semantically relevant experimental data and of performing relevant statistical testing for the retrieved data. Tissue Microarray (TMA) data are semantically rich and contains many biologically important hypotheses waiting for high throughput conclusions. Methods An application-specific ontology was developed for managing TMA and DNA microarray databases by semantic web technologies. Data were represented as Resource Description Framework (RDF) according to the framework of the ontology. Applications for hypothesis testing (Xperanto-RDF) for TMA data were designed and implemented by (1) formulating the syntactic and semantic structures of the hypotheses derived from TMA experiments, (2) formulating SPARQLs to reflect the semantic structures of the hypotheses, and (3) performing statistical test with the result sets returned by the SPARQLs. Results When a user designs a hypothesis in Xperanto-RDF and submits it, the hypothesis can be tested against TMA experimental data stored in Xperanto-RDF. When we evaluated four previously validated hypotheses as an illustration, all the hypotheses were supported by Xperanto-RDF. Conclusions We demonstrated the utility of high throughput biological hypothesis testing. We believe that preliminary investigation before performing highly controlled experiment can be benefited. PMID:21342584

Towards a Semantic Web of Things: A Hybrid Semantic Annotation, Extraction, and Reasoning Framework for Cyber-Physical System

PubMed Central

Wu, Zhenyu; Xu, Yuan; Yang, Yunong; Zhang, Chunhong; Zhu, Xinning; Ji, Yang

2017-01-01

Web of Things (WoT) facilitates the discovery and interoperability of Internet of Things (IoT) devices in a cyber-physical system (CPS). Moreover, a uniform knowledge representation of physical resources is quite necessary for further composition, collaboration, and decision-making process in CPS. Though several efforts have integrated semantics with WoT, such as knowledge engineering methods based on semantic sensor networks (SSN), it still could not represent the complex relationships between devices when dynamic composition and collaboration occur, and it totally depends on manual construction of a knowledge base with low scalability. In this paper, to addresses these limitations, we propose the semantic Web of Things (SWoT) framework for CPS (SWoT4CPS). SWoT4CPS provides a hybrid solution with both ontological engineering methods by extending SSN and machine learning methods based on an entity linking (EL) model. To testify to the feasibility and performance, we demonstrate the framework by implementing a temperature anomaly diagnosis and automatic control use case in a building automation system. Evaluation results on the EL method show that linking domain knowledge to DBpedia has a relative high accuracy and the time complexity is at a tolerant level. Advantages and disadvantages of SWoT4CPS with future work are also discussed. PMID:28230725

Semantic Service Design for Collaborative Business Processes in Internetworked Enterprises

NASA Astrophysics Data System (ADS)

Bianchini, Devis; Cappiello, Cinzia; de Antonellis, Valeria; Pernici, Barbara

Modern collaborating enterprises can be seen as borderless organizations whose processes are dynamically transformed and integrated with the ones of their partners (Internetworked Enterprises, IE), thus enabling the design of collaborative business processes. The adoption of Semantic Web and service-oriented technologies for implementing collaboration in such distributed and heterogeneous environments promises significant benefits. IE can model their own processes independently by using the Software as a Service paradigm (SaaS). Each enterprise maintains a catalog of available services and these can be shared across IE and reused to build up complex collaborative processes. Moreover, each enterprise can adopt its own terminology and concepts to describe business processes and component services. This brings requirements to manage semantic heterogeneity in process descriptions which are distributed across different enterprise systems. To enable effective service-based collaboration, IEs have to standardize their process descriptions and model them through component services using the same approach and principles. For enabling collaborative business processes across IE, services should be designed following an homogeneous approach, possibly maintaining a uniform level of granularity. In the paper we propose an ontology-based semantic modeling approach apt to enrich and reconcile semantics of process descriptions to facilitate process knowledge management and to enable semantic service design (by discovery, reuse and integration of process elements/constructs). The approach brings together Semantic Web technologies, techniques in process modeling, ontology building and semantic matching in order to provide a comprehensive semantic modeling framework.

Network-based approaches to climate knowledge discovery

NASA Astrophysics Data System (ADS)

Budich, Reinhard; Nyberg, Per; Weigel, Tobias

2011-11-01

Climate Knowledge Discovery Workshop; Hamburg, Germany, 30 March to 1 April 2011 Do complex networks combined with semantic Web technologies offer the next generation of solutions in climate science? To address this question, a first Climate Knowledge Discovery (CKD) Workshop, hosted by the German Climate Computing Center (Deutsches Klimarechenzentrum (DKRZ)), brought together climate and computer scientists from major American and European laboratories, data centers, and universities, as well as representatives from industry, the broader academic community, and the semantic Web communities. The participants, representing six countries, were concerned with large-scale Earth system modeling and computational data analysis. The motivation for the meeting was the growing problem that climate scientists generate data faster than it can be interpreted and the need to prepare for further exponential data increases. Current analysis approaches are focused primarily on traditional methods, which are best suited for large-scale phenomena and coarse-resolution data sets. The workshop focused on the open discussion of ideas and technologies to provide the next generation of solutions to cope with the increasing data volumes in climate science.

Mechanism-based Pharmacovigilance over the Life Sciences Linked Open Data Cloud.

PubMed

Kamdar, Maulik R; Musen, Mark A

2017-01-01

Adverse drug reactions (ADR) result in significant morbidity and mortality in patients, and a substantial proportion of these ADRs are caused by drug-drug interactions (DDIs). Pharmacovigilance methods are used to detect unanticipated DDIs and ADRs by mining Spontaneous Reporting Systems, such as the US FDA Adverse Event Reporting System (FAERS). However, these methods do not provide mechanistic explanations for the discovered drug-ADR associations in a systematic manner. In this paper, we present a systems pharmacology-based approach to perform mechanism-based pharmacovigilance. We integrate data and knowledge from four different sources using Semantic Web Technologies and Linked Data principles to generate a systems network. We present a network-based Apriori algorithm for association mining in FAERS reports. We evaluate our method against existing pharmacovigilance methods for three different validation sets. Our method has AUROC statistics of 0.7-0.8, similar to current methods, and event-specific thresholds generate AUROC statistics greater than 0.75 for certain ADRs. Finally, we discuss the benefits of using Semantic Web technologies to attain the objectives for mechanism-based pharmacovigilance.

Semantic Web, Reusable Learning Objects, Personal Learning Networks in Health: Key Pieces for Digital Health Literacy.

PubMed

Konstantinidis, Stathis Th; Wharrad, Heather; Windle, Richard; Bamidis, Panagiotis D

2017-01-01

The knowledge existing in the World Wide Web is exponentially expanding, while continuous advancements in health sciences contribute to the creation of new knowledge. There are a lot of efforts trying to identify how the social connectivity can endorse patients' empowerment, while other studies look at the identification and the quality of online materials. However, emphasis has not been put on the big picture of connecting the existing resources with the patients "new habits" of learning through their own Personal Learning Networks. In this paper we propose a framework for empowering patients' digital health literacy adjusted to patients' currents needs by utilizing the contemporary way of learning through Personal Learning Networks, existing high quality learning resources and semantics technologies for interconnecting knowledge pieces. The framework based on the concept of knowledge maps for health as defined in this paper. Health Digital Literacy needs definitely further enhancement and the use of the proposed concept might lead to useful tools which enable use of understandable health trusted resources tailored to each person needs.

Making species checklists understandable to machines - a shift from relational databases to ontologies.

PubMed

Laurenne, Nina; Tuominen, Jouni; Saarenmaa, Hannu; Hyvönen, Eero

2014-01-01

The scientific names of plants and animals play a major role in Life Sciences as information is indexed, integrated, and searched using scientific names. The main problem with names is their ambiguous nature, because more than one name may point to the same taxon and multiple taxa may share the same name. In addition, scientific names change over time, which makes them open to various interpretations. Applying machine-understandable semantics to these names enables efficient processing of biological content in information systems. The first step is to use unique persistent identifiers instead of name strings when referring to taxa. The most commonly used identifiers are Life Science Identifiers (LSID), which are traditionally used in relational databases, and more recently HTTP URIs, which are applied on the Semantic Web by Linked Data applications. We introduce two models for expressing taxonomic information in the form of species checklists. First, we show how species checklists are presented in a relational database system using LSIDs. Then, in order to gain a more detailed representation of taxonomic information, we introduce meta-ontology TaxMeOn to model the same content as Semantic Web ontologies where taxa are identified using HTTP URIs. We also explore how changes in scientific names can be managed over time. The use of HTTP URIs is preferable for presenting the taxonomic information of species checklists. An HTTP URI identifies a taxon and operates as a web address from which additional information about the taxon can be located, unlike LSID. This enables the integration of biological data from different sources on the web using Linked Data principles and prevents the formation of information silos. The Linked Data approach allows a user to assemble information and evaluate the complexity of taxonomical data based on conflicting views of taxonomic classifications. Using HTTP URIs and Semantic Web technologies also facilitate the representation of the semantics of biological data, and in this way, the creation of more "intelligent" biological applications and services.

AlzPharm: integration of neurodegeneration data using RDF.

PubMed

Lam, Hugo Y K; Marenco, Luis; Clark, Tim; Gao, Yong; Kinoshita, June; Shepherd, Gordon; Miller, Perry; Wu, Elizabeth; Wong, Gwendolyn T; Liu, Nian; Crasto, Chiquito; Morse, Thomas; Stephens, Susie; Cheung, Kei-Hoi

2007-05-09

Neuroscientists often need to access a wide range of data sets distributed over the Internet. These data sets, however, are typically neither integrated nor interoperable, resulting in a barrier to answering complex neuroscience research questions. Domain ontologies can enable the querying heterogeneous data sets, but they are not sufficient for neuroscience since the data of interest commonly span multiple research domains. To this end, e-Neuroscience seeks to provide an integrated platform for neuroscientists to discover new knowledge through seamless integration of the very diverse types of neuroscience data. Here we present a Semantic Web approach to building this e-Neuroscience framework by using the Resource Description Framework (RDF) and its vocabulary description language, RDF Schema (RDFS), as a standard data model to facilitate both representation and integration of the data. We have constructed a pilot ontology for BrainPharm (a subset of SenseLab) using RDFS and then converted a subset of the BrainPharm data into RDF according to the ontological structure. We have also integrated the converted BrainPharm data with existing RDF hypothesis and publication data from a pilot version of SWAN (Semantic Web Applications in Neuromedicine). Our implementation uses the RDF Data Model in Oracle Database 10g release 2 for data integration, query, and inference, while our Web interface allows users to query the data and retrieve the results in a convenient fashion. Accessing and integrating biomedical data which cuts across multiple disciplines will be increasingly indispensable and beneficial to neuroscience researchers. The Semantic Web approach we undertook has demonstrated a promising way to semantically integrate data sets created independently. It also shows how advanced queries and inferences can be performed over the integrated data, which are hard to achieve using traditional data integration approaches. Our pilot results suggest that our Semantic Web approach is suitable for realizing e-Neuroscience and generic enough to be applied in other biomedical fields.

AlzPharm: integration of neurodegeneration data using RDF

PubMed Central

Lam, Hugo YK; Marenco, Luis; Clark, Tim; Gao, Yong; Kinoshita, June; Shepherd, Gordon; Miller, Perry; Wu, Elizabeth; Wong, Gwendolyn T; Liu, Nian; Crasto, Chiquito; Morse, Thomas; Stephens, Susie; Cheung, Kei-Hoi

2007-01-01

Background Neuroscientists often need to access a wide range of data sets distributed over the Internet. These data sets, however, are typically neither integrated nor interoperable, resulting in a barrier to answering complex neuroscience research questions. Domain ontologies can enable the querying heterogeneous data sets, but they are not sufficient for neuroscience since the data of interest commonly span multiple research domains. To this end, e-Neuroscience seeks to provide an integrated platform for neuroscientists to discover new knowledge through seamless integration of the very diverse types of neuroscience data. Here we present a Semantic Web approach to building this e-Neuroscience framework by using the Resource Description Framework (RDF) and its vocabulary description language, RDF Schema (RDFS), as a standard data model to facilitate both representation and integration of the data. Results We have constructed a pilot ontology for BrainPharm (a subset of SenseLab) using RDFS and then converted a subset of the BrainPharm data into RDF according to the ontological structure. We have also integrated the converted BrainPharm data with existing RDF hypothesis and publication data from a pilot version of SWAN (Semantic Web Applications in Neuromedicine). Our implementation uses the RDF Data Model in Oracle Database 10g release 2 for data integration, query, and inference, while our Web interface allows users to query the data and retrieve the results in a convenient fashion. Conclusion Accessing and integrating biomedical data which cuts across multiple disciplines will be increasingly indispensable and beneficial to neuroscience researchers. The Semantic Web approach we undertook has demonstrated a promising way to semantically integrate data sets created independently. It also shows how advanced queries and inferences can be performed over the integrated data, which are hard to achieve using traditional data integration approaches. Our pilot results suggest that our Semantic Web approach is suitable for realizing e-Neuroscience and generic enough to be applied in other biomedical fields. PMID:17493287

Application of the Financial Industry Business Ontology (FIBO) for development of a financial organization ontology

NASA Astrophysics Data System (ADS)

Petrova, G. G.; Tuzovsky, A. F.; Aksenova, N. V.

2017-01-01

The article considers an approach to a formalized description and meaning harmonization for financial terms and means of semantic modeling. Ontologies for the semantic models are described with the help of special languages developed for the Semantic Web. Results of FIBO application to solution of different tasks in the Russian financial sector are given.

Component, Context, and Manufacturing Model Library (C2M2L)

DTIC Science & Technology

2012-11-01

123 5.1 MML Population and Web Service Interface...104 Table 41. Relevant Questions with Associated Web Services...the models, and implementing web services that provide semantically aware programmatic access to the models, including implementing the MS&T

Chemical Entity Semantic Specification: Knowledge representation for efficient semantic cheminformatics and facile data integration

PubMed Central

2011-01-01

Background Over the past several centuries, chemistry has permeated virtually every facet of human lifestyle, enriching fields as diverse as medicine, agriculture, manufacturing, warfare, and electronics, among numerous others. Unfortunately, application-specific, incompatible chemical information formats and representation strategies have emerged as a result of such diverse adoption of chemistry. Although a number of efforts have been dedicated to unifying the computational representation of chemical information, disparities between the various chemical databases still persist and stand in the way of cross-domain, interdisciplinary investigations. Through a common syntax and formal semantics, Semantic Web technology offers the ability to accurately represent, integrate, reason about and query across diverse chemical information. Results Here we specify and implement the Chemical Entity Semantic Specification (CHESS) for the representation of polyatomic chemical entities, their substructures, bonds, atoms, and reactions using Semantic Web technologies. CHESS provides means to capture aspects of their corresponding chemical descriptors, connectivity, functional composition, and geometric structure while specifying mechanisms for data provenance. We demonstrate that using our readily extensible specification, it is possible to efficiently integrate multiple disparate chemical data sources, while retaining appropriate correspondence of chemical descriptors, with very little additional effort. We demonstrate the impact of some of our representational decisions on the performance of chemically-aware knowledgebase searching and rudimentary reaction candidate selection. Finally, we provide access to the tools necessary to carry out chemical entity encoding in CHESS, along with a sample knowledgebase. Conclusions By harnessing the power of Semantic Web technologies with CHESS, it is possible to provide a means of facile cross-domain chemical knowledge integration with full preservation of data correspondence and provenance. Our representation builds on existing cheminformatics technologies and, by the virtue of RDF specification, remains flexible and amenable to application- and domain-specific annotations without compromising chemical data integration. We conclude that the adoption of a consistent and semantically-enabled chemical specification is imperative for surviving the coming chemical data deluge and supporting systems science research. PMID:21595881

Chemical Entity Semantic Specification: Knowledge representation for efficient semantic cheminformatics and facile data integration.

PubMed

Chepelev, Leonid L; Dumontier, Michel

2011-05-19

Over the past several centuries, chemistry has permeated virtually every facet of human lifestyle, enriching fields as diverse as medicine, agriculture, manufacturing, warfare, and electronics, among numerous others. Unfortunately, application-specific, incompatible chemical information formats and representation strategies have emerged as a result of such diverse adoption of chemistry. Although a number of efforts have been dedicated to unifying the computational representation of chemical information, disparities between the various chemical databases still persist and stand in the way of cross-domain, interdisciplinary investigations. Through a common syntax and formal semantics, Semantic Web technology offers the ability to accurately represent, integrate, reason about and query across diverse chemical information. Here we specify and implement the Chemical Entity Semantic Specification (CHESS) for the representation of polyatomic chemical entities, their substructures, bonds, atoms, and reactions using Semantic Web technologies. CHESS provides means to capture aspects of their corresponding chemical descriptors, connectivity, functional composition, and geometric structure while specifying mechanisms for data provenance. We demonstrate that using our readily extensible specification, it is possible to efficiently integrate multiple disparate chemical data sources, while retaining appropriate correspondence of chemical descriptors, with very little additional effort. We demonstrate the impact of some of our representational decisions on the performance of chemically-aware knowledgebase searching and rudimentary reaction candidate selection. Finally, we provide access to the tools necessary to carry out chemical entity encoding in CHESS, along with a sample knowledgebase. By harnessing the power of Semantic Web technologies with CHESS, it is possible to provide a means of facile cross-domain chemical knowledge integration with full preservation of data correspondence and provenance. Our representation builds on existing cheminformatics technologies and, by the virtue of RDF specification, remains flexible and amenable to application- and domain-specific annotations without compromising chemical data integration. We conclude that the adoption of a consistent and semantically-enabled chemical specification is imperative for surviving the coming chemical data deluge and supporting systems science research.

Exposing Coverage Data to the Semantic Web within the MELODIES project: Challenges and Solutions

NASA Astrophysics Data System (ADS)

Riechert, Maik; Blower, Jon; Griffiths, Guy

2016-04-01

Coverage data, typically big in data volume, assigns values to a given set of spatiotemporal positions, together with metadata on how to interpret those values. Existing storage formats like netCDF, HDF and GeoTIFF all have various restrictions that prevent them from being preferred formats for use over the web, especially the semantic web. Factors that are relevant here are the processing complexity, the semantic richness of the metadata, and the ability to request partial information, such as a subset or just the appropriate metadata. Making coverage data available within web browsers opens the door to new ways for working with such data, including new types of visualization and on-the-fly processing. As part of the European project MELODIES (http://melodiesproject.eu) we look into the challenges of exposing such coverage data in an interoperable and web-friendly way, and propose solutions using a host of emerging technologies like JSON-LD, the DCAT and GeoDCAT-AP ontologies, the CoverageJSON format, and new approaches to REST APIs for coverage data. We developed the CoverageJSON format within the MELODIES project as an additional way to expose coverage data to the web, next to having simple rendered images available using standards like OGC's WMS. CoverageJSON partially incorporates JSON-LD but does not encode individual data values as semantic resources, making use of the technology in a practical manner. The development also focused on it being a potential output format for OGC WCS. We will demonstrate how existing netCDF data can be exposed as CoverageJSON resources on the web together with a REST API that allows users to explore the data and run operations such as spatiotemporal subsetting. We will show various use cases from the MELODIES project, including reclassification of a Land Cover dataset client-side within the browser with the ability for the user to influence the reclassification result by making use of the above technologies.

The SADI Personal Health Lens: A Web Browser-Based System for Identifying Personally Relevant Drug Interactions.

PubMed

Vandervalk, Ben; McCarthy, E Luke; Cruz-Toledo, José; Klein, Artjom; Baker, Christopher J O; Dumontier, Michel; Wilkinson, Mark D

2013-04-05

The Web provides widespread access to vast quantities of health-related information that can improve quality-of-life through better understanding of personal symptoms, medical conditions, and available treatments. Unfortunately, identifying a credible and personally relevant subset of information can be a time-consuming and challenging task for users without a medical background. The objective of the Personal Health Lens system is to aid users when reading health-related webpages by providing warnings about personally relevant drug interactions. More broadly, we wish to present a prototype for a novel, generalizable approach to facilitating interactions between a patient, their practitioner(s), and the Web. We utilized a distributed, Semantic Web-based architecture for recognizing personally dangerous drugs consisting of: (1) a private, local triple store of personal health information, (2) Semantic Web services, following the Semantic Automated Discovery and Integration (SADI) design pattern, for text mining and identifying substance interactions, (3) a bookmarklet to trigger analysis of a webpage and annotate it with personalized warnings, and (4) a semantic query that acts as an abstract template of the analytical workflow to be enacted by the system. A prototype implementation of the system is provided in the form of a Java standalone executable JAR file. The JAR file bundles all components of the system: the personal health database, locally-running versions of the SADI services, and a javascript bookmarklet that triggers analysis of a webpage. In addition, the demonstration includes a hypothetical personal health profile, allowing the system to be used immediately without configuration. Usage instructions are provided. The main strength of the Personal Health Lens system is its ability to organize medical information and to present it to the user in a personalized and contextually relevant manner. While this prototype was limited to a single knowledge domain (drug/drug interactions), the proposed architecture is generalizable, and could act as the foundation for much richer personalized-health-Web clients, while importantly providing a novel and personalizable mechanism for clinical experts to inject their expertise into the browsing experience of their patients in the form of customized semantic queries and ontologies.

The SADI Personal Health Lens: A Web Browser-Based System for Identifying Personally Relevant Drug Interactions

PubMed Central

Vandervalk, Ben; McCarthy, E Luke; Cruz-Toledo, José; Klein, Artjom; Baker, Christopher J O; Dumontier, Michel

2013-01-01

Background The Web provides widespread access to vast quantities of health-related information that can improve quality-of-life through better understanding of personal symptoms, medical conditions, and available treatments. Unfortunately, identifying a credible and personally relevant subset of information can be a time-consuming and challenging task for users without a medical background. Objective The objective of the Personal Health Lens system is to aid users when reading health-related webpages by providing warnings about personally relevant drug interactions. More broadly, we wish to present a prototype for a novel, generalizable approach to facilitating interactions between a patient, their practitioner(s), and the Web. Methods We utilized a distributed, Semantic Web-based architecture for recognizing personally dangerous drugs consisting of: (1) a private, local triple store of personal health information, (2) Semantic Web services, following the Semantic Automated Discovery and Integration (SADI) design pattern, for text mining and identifying substance interactions, (3) a bookmarklet to trigger analysis of a webpage and annotate it with personalized warnings, and (4) a semantic query that acts as an abstract template of the analytical workflow to be enacted by the system. Results A prototype implementation of the system is provided in the form of a Java standalone executable JAR file. The JAR file bundles all components of the system: the personal health database, locally-running versions of the SADI services, and a javascript bookmarklet that triggers analysis of a webpage. In addition, the demonstration includes a hypothetical personal health profile, allowing the system to be used immediately without configuration. Usage instructions are provided. Conclusions The main strength of the Personal Health Lens system is its ability to organize medical information and to present it to the user in a personalized and contextually relevant manner. While this prototype was limited to a single knowledge domain (drug/drug interactions), the proposed architecture is generalizable, and could act as the foundation for much richer personalized-health-Web clients, while importantly providing a novel and personalizable mechanism for clinical experts to inject their expertise into the browsing experience of their patients in the form of customized semantic queries and ontologies. PMID:23612187

DisGeNET: a discovery platform for the dynamical exploration of human diseases and their genes.

PubMed

Piñero, Janet; Queralt-Rosinach, Núria; Bravo, Àlex; Deu-Pons, Jordi; Bauer-Mehren, Anna; Baron, Martin; Sanz, Ferran; Furlong, Laura I

2015-01-01

DisGeNET is a comprehensive discovery platform designed to address a variety of questions concerning the genetic underpinning of human diseases. DisGeNET contains over 380,000 associations between >16,000 genes and 13,000 diseases, which makes it one of the largest repositories currently available of its kind. DisGeNET integrates expert-curated databases with text-mined data, covers information on Mendelian and complex diseases, and includes data from animal disease models. It features a score based on the supporting evidence to prioritize gene-disease associations. It is an open access resource available through a web interface, a Cytoscape plugin and as a Semantic Web resource. The web interface supports user-friendly data exploration and navigation. DisGeNET data can also be analysed via the DisGeNET Cytoscape plugin, and enriched with the annotations of other plugins of this popular network analysis software suite. Finally, the information contained in DisGeNET can be expanded and complemented using Semantic Web technologies and linked to a variety of resources already present in the Linked Data cloud. Hence, DisGeNET offers one of the most comprehensive collections of human gene-disease associations and a valuable set of tools for investigating the molecular mechanisms underlying diseases of genetic origin, designed to fulfill the needs of different user profiles, including bioinformaticians, biologists and health-care practitioners. Database URL: http://www.disgenet.org/ © The Author(s) 2015. Published by Oxford University Press.

Generation of open biomedical datasets through ontology-driven transformation and integration processes.

PubMed

Carmen Legaz-García, María Del; Miñarro-Giménez, José Antonio; Menárguez-Tortosa, Marcos; Fernández-Breis, Jesualdo Tomás

2016-06-03

Biomedical research usually requires combining large volumes of data from multiple heterogeneous sources, which makes difficult the integrated exploitation of such data. The Semantic Web paradigm offers a natural technological space for data integration and exploitation by generating content readable by machines. Linked Open Data is a Semantic Web initiative that promotes the publication and sharing of data in machine readable semantic formats. We present an approach for the transformation and integration of heterogeneous biomedical data with the objective of generating open biomedical datasets in Semantic Web formats. The transformation of the data is based on the mappings between the entities of the data schema and the ontological infrastructure that provides the meaning to the content. Our approach permits different types of mappings and includes the possibility of defining complex transformation patterns. Once the mappings are defined, they can be automatically applied to datasets to generate logically consistent content and the mappings can be reused in further transformation processes. The results of our research are (1) a common transformation and integration process for heterogeneous biomedical data; (2) the application of Linked Open Data principles to generate interoperable, open, biomedical datasets; (3) a software tool, called SWIT, that implements the approach. In this paper we also describe how we have applied SWIT in different biomedical scenarios and some lessons learned. We have presented an approach that is able to generate open biomedical repositories in Semantic Web formats. SWIT is able to apply the Linked Open Data principles in the generation of the datasets, so allowing for linking their content to external repositories and creating linked open datasets. SWIT datasets may contain data from multiple sources and schemas, thus becoming integrated datasets.

Actionable, long-term stable and semantic web compatible identifiers for access to biological collection objects

PubMed Central

Hyam, Roger; Hagedorn, Gregor; Chagnoux, Simon; Röpert, Dominik; Casino, Ana; Droege, Gabi; Glöckler, Falko; Gödderz, Karsten; Groom, Quentin; Hoffmann, Jana; Holleman, Ayco; Kempa, Matúš; Koivula, Hanna; Marhold, Karol; Nicolson, Nicky; Smith, Vincent S.; Triebel, Dagmar

2017-01-01

With biodiversity research activities being increasingly shifted to the web, the need for a system of persistent and stable identifiers for physical collection objects becomes increasingly pressing. The Consortium of European Taxonomic Facilities agreed on a common system of HTTP-URI-based stable identifiers which is now rolled out to its member organizations. The system follows Linked Open Data principles and implements redirection mechanisms to human-readable and machine-readable representations of specimens facilitating seamless integration into the growing semantic web. The implementation of stable identifiers across collection organizations is supported with open source provider software scripts, best practices documentations and recommendations for RDF metadata elements facilitating harmonized access to collection information in web portals. Database URL: http://cetaf.org/cetaf-stable-identifiers PMID:28365724

Using Semantic Web Technologies for Cohort Identification from Electronic Health Records for Clinical Research

PubMed Central

Pathak, Jyotishman; Kiefer, Richard C.; Chute, Christopher G.

2012-01-01

The ability to conduct genome-wide association studies (GWAS) has enabled new exploration of how genetic variations contribute to health and disease etiology. One of the key requirements to perform GWAS is the identification of subject cohorts with accurate classification of disease phenotypes. In this work, we study how emerging Semantic Web technologies can be applied in conjunction with clinical data stored in electronic health records (EHRs) to accurately identify subjects with specific diseases for inclusion in cohort studies. In particular, we demonstrate the role of using Resource Description Framework (RDF) for representing EHR data and enabling federated querying and inferencing via standardized Web protocols for identifying subjects with Diabetes Mellitus. Our study highlights the potential of using Web-scale data federation approaches to execute complex queries. PMID:22779040

Semantics-enabled service discovery framework in the SIMDAT pharma grid.

PubMed

Qu, Cangtao; Zimmermann, Falk; Kumpf, Kai; Kamuzinzi, Richard; Ledent, Valérie; Herzog, Robert

2008-03-01

We present the design and implementation of a semantics-enabled service discovery framework in the data Grids for process and product development using numerical simulation and knowledge discovery (SIMDAT) Pharma Grid, an industry-oriented Grid environment for integrating thousands of Grid-enabled biological data services and analysis services. The framework consists of three major components: the Web ontology language (OWL)-description logic (DL)-based biological domain ontology, OWL Web service ontology (OWL-S)-based service annotation, and semantic matchmaker based on the ontology reasoning. Built upon the framework, workflow technologies are extensively exploited in the SIMDAT to assist biologists in (semi)automatically performing in silico experiments. We present a typical usage scenario through the case study of a biological workflow: IXodus.

Ontology development for provenance tracing in National Climate Assessment of the US Global Change Research Program

NASA Astrophysics Data System (ADS)

Ma, X.; Zheng, J. G.; Goldstein, J.; Duggan, B.; Xu, J.; Du, C.; Akkiraju, A.; Aulenbach, S.; Tilmes, C.; Fox, P. A.

2013-12-01

The periodical National Climate Assessment (NCA) of the US Global Change Research Program (USGCRP) [1] produces reports about findings of global climate change and the impacts of climate change on the United States. Those findings are of great public and academic concerns and are used in policy and management decisions, which make the provenance information of findings in those reports especially important. The USGCRP is developing a Global Change Information System (GCIS), in which the NCA reports and associated provenance information are the primary records. We were modeling and developing Semantic Web applications for the GCIS. By applying a use case-driven iterative methodology [2], we developed an ontology [3] to represent the content structure of a report and the associated provenance information. We also mapped the classes and properties in our ontology into the W3C PROV-O ontology [4] to realize the formal presentation of provenance. We successfully implemented the ontology in several pilot systems for a recent National Climate Assessment report (i.e., the NCA3). They provide users the functionalities to browse and search provenance information with topics of interest. Provenance information of the NCA3 has been made structured and interoperable by applying the developed ontology. Besides the pilot systems we developed, other tools and services are also able to interact with the data in the context of the 'Web of data' and thus create added values. Our research shows that the use case-driven iterative method bridges the gap between Semantic Web researchers and earth and environmental scientists and is able to be deployed rapidly for developing Semantic Web applications. Our work also provides first-hand experience for re-using the W3C PROV-O ontology in the field of earth and environmental sciences, as the PROV-O ontology is recently ratified (on 04/30/2013) by the W3C as a recommendation and relevant applications are still rare. [1] http://www.globalchange.gov [2] Fox, P., McGuinness, D.L., 2008. TWC Semantic Web Methodology. Accessible at: http://tw.rpi.edu/web/doc/TWC_SemanticWebMethodology [3] https://scm.escience.rpi.edu/svn/public/projects/gcis/trunk/rdf/schema/GCISOntology.ttl [4] http://www.w3.org/TR/prov-o/

Knowledge-driven enhancements for task composition in bioinformatics.

PubMed

Sutherland, Karen; McLeod, Kenneth; Ferguson, Gus; Burger, Albert

2009-10-01

A key application area of semantic technologies is the fast-developing field of bioinformatics. Sealife was a project within this field with the aim of creating semantics-based web browsing capabilities for the Life Sciences. This includes meaningfully linking significant terms from the text of a web page to executable web services. It also involves the semantic mark-up of biological terms, linking them to biomedical ontologies, then discovering and executing services based on terms that interest the user. A system was produced which allows a user to identify terms of interest on a web page and subsequently connects these to a choice of web services which can make use of these inputs. Elements of Artificial Intelligence Planning build on this to present a choice of higher level goals, which can then be broken down to construct a workflow. An Argumentation System was implemented to evaluate the results produced by three different gene expression databases. An evaluation of these modules was carried out on users from a variety of backgrounds. Users with little knowledge of web services were able to achieve tasks that used several services in much less time than they would have taken to do this manually. The Argumentation System was also considered a useful resource and feedback was collected on the best way to present results. Overall the system represents a move forward in helping users to both construct workflows and analyse results by incorporating specific domain knowledge into the software. It also provides a mechanism by which web pages can be linked to web services. However, this work covers a specific domain and much co-ordinated effort is needed to make all web services available for use in such a way, i.e. the integration of underlying knowledge is a difficult but essential task.

NCI's national environmental research data collection: metadata management built on standards and preparing for the semantic web

NASA Astrophysics Data System (ADS)

Wang, Jingbo; Bastrakova, Irina; Evans, Ben; Gohar, Kashif; Santana, Fabiana; Wyborn, Lesley

2015-04-01

National Computational Infrastructure (NCI) manages national environmental research data collections (10+ PB) as part of its specialized high performance data node of the Research Data Storage Infrastructure (RDSI) program. We manage 40+ data collections using NCI's Data Management Plan (DMP), which is compatible with the ISO 19100 metadata standards. We utilize ISO standards to make sure our metadata is transferable and interoperable for sharing and harvesting. The DMP is used along with metadata from the data itself, to create a hierarchy of data collection, dataset and time series catalogues that is then exposed through GeoNetwork for standard discoverability. This hierarchy catalogues are linked using a parent-child relationship. The hierarchical infrastructure of our GeoNetwork catalogues system aims to address both discoverability and in-house administrative use-cases. At NCI, we are currently improving the metadata interoperability in our catalogue by linking with standardized community vocabulary services. These emerging vocabulary services are being established to help harmonise data from different national and international scientific communities. One such vocabulary service is currently being established by the Australian National Data Services (ANDS). Data citation is another important aspect of the NCI data infrastructure, which allows tracking of data usage and infrastructure investment, encourage data sharing, and increasing trust in research that is reliant on these data collections. We incorporate the standard vocabularies into the data citation metadata so that the data citation become machine readable and semantically friendly for web-search purpose as well. By standardizing our metadata structure across our entire data corpus, we are laying the foundation to enable the application of appropriate semantic mechanisms to enhance discovery and analysis of NCI's national environmental research data information. We expect that this will further increase the data discoverability and encourage the data sharing and reuse within the community, increasing the value of the data much further than its current use.

Mining Genotype-Phenotype Associations from Public Knowledge Sources via Semantic Web Querying

PubMed Central

Kiefer, Richard C.; Freimuth, Robert R.; Chute, Christopher G; Pathak, Jyotishman

Gene Wiki Plus (GeneWiki+) and the Online Mendelian Inheritance in Man (OMIM) are publicly available resources for sharing information about disease-gene and gene-SNP associations in humans. While immensely useful to the scientific community, both resources are manually curated, thereby making the data entry and publication process time-consuming, and to some degree, error-prone. To this end, this study investigates Semantic Web technologies to validate existing and potentially discover new genotype-phenotype associations in GWP and OMIM. In particular, we demonstrate the applicability of SPARQL queries for identifying associations not explicitly stated for commonly occurring chronic diseases in GWP and OMIM, and report our preliminary findings for coverage, completeness, and validity of the associations. Our results highlight the benefits of Semantic Web querying technology to validate existing disease-gene associations as well as identify novel associations although further evaluation and analysis is required before such information can be applied and used effectively. PMID:24303249

SPARQL Assist language-neutral query composer

PubMed Central

2012-01-01

Background SPARQL query composition is difficult for the lay-person, and even the experienced bioinformatician in cases where the data model is unfamiliar. Moreover, established best-practices and internationalization concerns dictate that the identifiers for ontological terms should be opaque rather than human-readable, which further complicates the task of synthesizing queries manually. Results We present SPARQL Assist: a Web application that addresses these issues by providing context-sensitive type-ahead completion during SPARQL query construction. Ontological terms are suggested using their multi-lingual labels and descriptions, leveraging existing support for internationalization and language-neutrality. Moreover, the system utilizes the semantics embedded in ontologies, and within the query itself, to help prioritize the most likely suggestions. Conclusions To ensure success, the Semantic Web must be easily available to all users, regardless of locale, training, or preferred language. By enhancing support for internationalization, and moreover by simplifying the manual construction of SPARQL queries through the use of controlled-natural-language interfaces, we believe we have made some early steps towards simplifying access to Semantic Web resources. PMID:22373327

SPARQL assist language-neutral query composer.

PubMed

McCarthy, Luke; Vandervalk, Ben; Wilkinson, Mark

2012-01-25

SPARQL query composition is difficult for the lay-person, and even the experienced bioinformatician in cases where the data model is unfamiliar. Moreover, established best-practices and internationalization concerns dictate that the identifiers for ontological terms should be opaque rather than human-readable, which further complicates the task of synthesizing queries manually. We present SPARQL Assist: a Web application that addresses these issues by providing context-sensitive type-ahead completion during SPARQL query construction. Ontological terms are suggested using their multi-lingual labels and descriptions, leveraging existing support for internationalization and language-neutrality. Moreover, the system utilizes the semantics embedded in ontologies, and within the query itself, to help prioritize the most likely suggestions. To ensure success, the Semantic Web must be easily available to all users, regardless of locale, training, or preferred language. By enhancing support for internationalization, and moreover by simplifying the manual construction of SPARQL queries through the use of controlled-natural-language interfaces, we believe we have made some early steps towards simplifying access to Semantic Web resources.

Exploration of SWRL Rule Bases through Visualization, Paraphrasing, and Categorization of Rules

NASA Astrophysics Data System (ADS)

Hassanpour, Saeed; O'Connor, Martin J.; Das, Amar K.

Rule bases are increasingly being used as repositories of knowledge content on the Semantic Web. As the size and complexity of these rule bases increases, developers and end users need methods of rule abstraction to facilitate rule management. In this paper, we describe a rule abstraction method for Semantic Web Rule Language (SWRL) rules that is based on lexical analysis and a set of heuristics. Our method results in a tree data structure that we exploit in creating techniques to visualize, paraphrase, and categorize SWRL rules. We evaluate our approach by applying it to several biomedical ontologies that contain SWRL rules, and show how the results reveal rule patterns within the rule base. We have implemented our method as a plug-in tool for Protégé-OWL, the most widely used ontology modeling software for the Semantic Web. Our tool can allow users to rapidly explore content and patterns in SWRL rule bases, enabling their acquisition and management.

Publishing high-quality climate data on the semantic web

NASA Astrophysics Data System (ADS)

Woolf, Andrew; Haller, Armin; Lefort, Laurent; Taylor, Kerry

2013-04-01

The effort over more than a decade to establish the semantic web [Berners-Lee et. al., 2001] has received a major boost in recent years through the Open Government movement. Governments around the world are seeking technical solutions to enable more open and transparent access to Public Sector Information (PSI) they hold. Existing technical protocols and data standards tend to be domain specific, and so limit the ability to publish and integrate data across domains (health, environment, statistics, education, etc.). The web provides a domain-neutral platform for information publishing, and has proven itself beyond expectations for publishing and linking human-readable electronic documents. Extending the web pattern to data (often called Web 3.0) offers enormous potential. The semantic web applies the basic web principles to data [Berners-Lee, 2006]: using URIs as identifiers (for data objects and real-world 'things', instead of documents) making the URIs actionable by providing useful information via HTTP using a common exchange standard (serialised RDF for data instead of HTML for documents) establishing typed links between information objects to enable linking and integration Leading examples of 'linked data' for publishing PSI may be found in both the UK (http://data.gov.uk/linked-data) and US (http://www.data.gov/page/semantic-web). The Bureau of Meteorology (BoM) is Australia's national meteorological agency, and has a new mandate to establish a national environmental information infrastructure (under the National Plan for Environmental Information, NPEI [BoM, 2012a]). While the initial approach is based on the existing best practice Spatial Data Infrastructure (SDI) architecture, linked-data is being explored as a technological alternative that shows great promise for the future. We report here the first trial of government linked-data in Australia under data.gov.au. In this initial pilot study, we have taken BoM's new high-quality reference surface temperature dataset, Australian Climate Observations Reference Network - Surface Air Temperature (ACORN-SAT) [BoM, 2012b]. This dataset contains daily homogenised surface temperature observations for 112 locations around Australia, dating back to 1910. An ontology for the dataset was developed [Lefort et. al., 2012], based on the existing Semantic Sensor Network ontology [Compton et. al., 2012] and the W3C RDF Data Cube vocabulary [W3C, 2012]. Additional vocabularies were developed, e.g. for BoM weather stations and rainfall districts. The dataset was converted to RDF and loaded into an RDF triplestore. The Linked-Data API (http://code.google.com/p/linked-data-api) was used to configure specific URI query patterns (e.g. for observation timeseries slices by station), and a SPARQL endpoint was provided for direct querying. In addition, some demonstration 'mash-ups' were developed, providing an interactive browser-based interface to the temperature timeseries. References [Berners-Lee et. al., 2001] Tim Berners-Lee, James Hendler and Ora Lassila (2001), "The Semantic Web", Scientific American, May 2001. [Berners-Lee, 2006] Tim Berners-Lee (2006), "Linked Data - Design Issues", W3C [http://www.w3.org/DesignIssues/LinkedData.html] [BoM, 2012a] Bureau of Meteorology (2012), "Environmental information" [http://www.bom.gov.au/environment/] [BoM, 2012b] Bureau of Meteorology (2012), "Australian Climate Observations Reference Network - Surface Air Temperature" [http://www.bom.gov.au/climate/change/acorn-sat/] [Compton et. al., 2012] Michael Compton, Payam Barnaghi, Luis Bermudez, Raul Garcia-Castro, Oscar Corcho, Simon Cox, John Graybeal, Manfred Hauswirth, Cory Henson, Arthur Herzog, Vincent Huang, Krzysztof Janowicz, W. David Kelsey, Danh Le Phuoc, Laurent Lefort, Myriam Leggieri, Holger Neuhaus, Andriy Nikolov, Kevin Page, Alexandre Passant, Amit Sheth, Kerry Taylor (2012), "The SSN Ontology of the W3C Semantic Sensor Network Incubator Group", J. Web Semantics, 17 (2012) [http://dx.doi.org/10.1016/j.websem.2012.05.003] [Lefort et. al., 2012] Laurent Lefort, Josh Bobruk, Armin Haller, Kerry Taylor and Andrew Woolf (2012), "A Linked Sensor Data Cube for a 100 Year Homogenised daily temperature dataset", Proc. Semantic Sensor Networks 2012 [http://ceur-ws.org/Vol-904/paper10.pdf] [W3C, 2012] W3C (2012), "The RDF Data Cube Vocabulary", [http://www.w3.org/TR/vocab-data-cube/

Ontology-Based Administration of Web Directories

NASA Astrophysics Data System (ADS)

Horvat, Marko; Gledec, Gordan; Bogunović, Nikola

Administration of a Web directory and maintenance of its content and the associated structure is a delicate and labor intensive task performed exclusively by human domain experts. Subsequently there is an imminent risk of a directory structures becoming unbalanced, uneven and difficult to use to all except for a few users proficient with the particular Web directory and its domain. These problems emphasize the need to establish two important issues: i) generic and objective measures of Web directories structure quality, and ii) mechanism for fully automated development of a Web directory's structure. In this paper we demonstrate how to formally and fully integrate Web directories with the Semantic Web vision. We propose a set of criteria for evaluation of a Web directory's structure quality. Some criterion functions are based on heuristics while others require the application of ontologies. We also suggest an ontology-based algorithm for construction of Web directories. By using ontologies to describe the semantics of Web resources and Web directories' categories it is possible to define algorithms that can build or rearrange the structure of a Web directory. Assessment procedures can provide feedback and help steer the ontology-based construction process. The issues raised in the article can be equally applied to new and existing Web directories.

Introducing glycomics data into the Semantic Web

PubMed Central

2013-01-01

Background Glycoscience is a research field focusing on complex carbohydrates (otherwise known as glycans)a, which can, for example, serve as “switches” that toggle between different functions of a glycoprotein or glycolipid. Due to the advancement of glycomics technologies that are used to characterize glycan structures, many glycomics databases are now publicly available and provide useful information for glycoscience research. However, these databases have almost no link to other life science databases. Results In order to implement support for the Semantic Web most efficiently for glycomics research, the developers of major glycomics databases agreed on a minimal standard for representing glycan structure and annotation information using RDF (Resource Description Framework). Moreover, all of the participants implemented this standard prototype and generated preliminary RDF versions of their data. To test the utility of the converted data, all of the data sets were uploaded into a Virtuoso triple store, and several SPARQL queries were tested as “proofs-of-concept” to illustrate the utility of the Semantic Web in querying across databases which were originally difficult to implement. Conclusions We were able to successfully retrieve information by linking UniCarbKB, GlycomeDB and JCGGDB in a single SPARQL query to obtain our target information. We also tested queries linking UniProt with GlycoEpitope as well as lectin data with GlycomeDB through PDB. As a result, we have been able to link proteomics data with glycomics data through the implementation of Semantic Web technologies, allowing for more flexible queries across these domains. PMID:24280648

Introducing glycomics data into the Semantic Web.

PubMed

Aoki-Kinoshita, Kiyoko F; Bolleman, Jerven; Campbell, Matthew P; Kawano, Shin; Kim, Jin-Dong; Lütteke, Thomas; Matsubara, Masaaki; Okuda, Shujiro; Ranzinger, Rene; Sawaki, Hiromichi; Shikanai, Toshihide; Shinmachi, Daisuke; Suzuki, Yoshinori; Toukach, Philip; Yamada, Issaku; Packer, Nicolle H; Narimatsu, Hisashi

2013-11-26

Glycoscience is a research field focusing on complex carbohydrates (otherwise known as glycans)a, which can, for example, serve as "switches" that toggle between different functions of a glycoprotein or glycolipid. Due to the advancement of glycomics technologies that are used to characterize glycan structures, many glycomics databases are now publicly available and provide useful information for glycoscience research. However, these databases have almost no link to other life science databases. In order to implement support for the Semantic Web most efficiently for glycomics research, the developers of major glycomics databases agreed on a minimal standard for representing glycan structure and annotation information using RDF (Resource Description Framework). Moreover, all of the participants implemented this standard prototype and generated preliminary RDF versions of their data. To test the utility of the converted data, all of the data sets were uploaded into a Virtuoso triple store, and several SPARQL queries were tested as "proofs-of-concept" to illustrate the utility of the Semantic Web in querying across databases which were originally difficult to implement. We were able to successfully retrieve information by linking UniCarbKB, GlycomeDB and JCGGDB in a single SPARQL query to obtain our target information. We also tested queries linking UniProt with GlycoEpitope as well as lectin data with GlycomeDB through PDB. As a result, we have been able to link proteomics data with glycomics data through the implementation of Semantic Web technologies, allowing for more flexible queries across these domains.

Quality evaluation of value sets from cancer study common data elements using the UMLS semantic groups

PubMed Central

Solbrig, Harold R; Chute, Christopher G

2012-01-01

Objective The objective of this study is to develop an approach to evaluate the quality of terminological annotations on the value set (ie, enumerated value domain) components of the common data elements (CDEs) in the context of clinical research using both unified medical language system (UMLS) semantic types and groups. Materials and methods The CDEs of the National Cancer Institute (NCI) Cancer Data Standards Repository, the NCI Thesaurus (NCIt) concepts and the UMLS semantic network were integrated using a semantic web-based framework for a SPARQL-enabled evaluation. First, the set of CDE-permissible values with corresponding meanings in external controlled terminologies were isolated. The corresponding value meanings were then evaluated against their NCI- or UMLS-generated semantic network mapping to determine whether all of the meanings fell within the same semantic group. Results Of the enumerated CDEs in the Cancer Data Standards Repository, 3093 (26.2%) had elements drawn from more than one UMLS semantic group. A random sample (n=100) of this set of elements indicated that 17% of them were likely to have been misclassified. Discussion The use of existing semantic web tools can support a high-throughput mechanism for evaluating the quality of large CDE collections. This study demonstrates that the involvement of multiple semantic groups in an enumerated value domain of a CDE is an effective anchor to trigger an auditing point for quality evaluation activities. Conclusion This approach produces a useful quality assurance mechanism for a clinical study CDE repository. PMID:22511016

Creating personalised clinical pathways by semantic interoperability with electronic health records.

PubMed

Wang, Hua-Qiong; Li, Jing-Song; Zhang, Yi-Fan; Suzuki, Muneou; Araki, Kenji

2013-06-01

There is a growing realisation that clinical pathways (CPs) are vital for improving the treatment quality of healthcare organisations. However, treatment personalisation is one of the main challenges when implementing CPs, and the inadequate dynamic adaptability restricts the practicality of CPs. The purpose of this study is to improve the practicality of CPs using semantic interoperability between knowledge-based CPs and semantic electronic health records (EHRs). Simple protocol and resource description framework query language is used to gather patient information from semantic EHRs. The gathered patient information is entered into the CP ontology represented by web ontology language. Then, after reasoning over rules described by semantic web rule language in the Jena semantic framework, we adjust the standardised CPs to meet different patients' practical needs. A CP for acute appendicitis is used as an example to illustrate how to achieve CP customisation based on the semantic interoperability between knowledge-based CPs and semantic EHRs. A personalised care plan is generated by comprehensively analysing the patient's personal allergy history and past medical history, which are stored in semantic EHRs. Additionally, by monitoring the patient's clinical information, an exception is recorded and handled during CP execution. According to execution results of the actual example, the solutions we present are shown to be technically feasible. This study contributes towards improving the clinical personalised practicality of standardised CPs. In addition, this study establishes the foundation for future work on the research and development of an independent CP system. Copyright © 2013 Elsevier B.V. All rights reserved.

Web-based Visualization and Query of semantically segmented multiresolution 3D Models in the Field of Cultural Heritage

NASA Astrophysics Data System (ADS)

Auer, M.; Agugiaro, G.; Billen, N.; Loos, L.; Zipf, A.

2014-05-01

Many important Cultural Heritage sites have been studied over long periods of time by different means of technical equipment, methods and intentions by different researchers. This has led to huge amounts of heterogeneous "traditional" datasets and formats. The rising popularity of 3D models in the field of Cultural Heritage in recent years has brought additional data formats and makes it even more necessary to find solutions to manage, publish and study these data in an integrated way. The MayaArch3D project aims to realize such an integrative approach by establishing a web-based research platform bringing spatial and non-spatial databases together and providing visualization and analysis tools. Especially the 3D components of the platform use hierarchical segmentation concepts to structure the data and to perform queries on semantic entities. This paper presents a database schema to organize not only segmented models but also different Levels-of-Details and other representations of the same entity. It is further implemented in a spatial database which allows the storing of georeferenced 3D data. This enables organization and queries by semantic, geometric and spatial properties. As service for the delivery of the segmented models a standardization candidate of the OpenGeospatialConsortium (OGC), the Web3DService (W3DS) has been extended to cope with the new database schema and deliver a web friendly format for WebGL rendering. Finally a generic user interface is presented which uses the segments as navigation metaphor to browse and query the semantic segmentation levels and retrieve information from an external database of the German Archaeological Institute (DAI).

Convergence of Health Level Seven Version 2 Messages to Semantic Web Technologies for Software-Intensive Systems in Telemedicine Trauma Care.

PubMed

Menezes, Pedro Monteiro; Cook, Timothy Wayne; Cavalini, Luciana Tricai

2016-01-01

To present the technical background and the development of a procedure that enriches the semantics of Health Level Seven version 2 (HL7v2) messages for software-intensive systems in telemedicine trauma care. This study followed a multilevel model-driven approach for the development of semantically interoperable health information systems. The Pre-Hospital Trauma Life Support (PHTLS) ABCDE protocol was adopted as the use case. A prototype application embedded the semantics into an HL7v2 message as an eXtensible Markup Language (XML) file, which was validated against an XML schema that defines constraints on a common reference model. This message was exchanged with a second prototype application, developed on the Mirth middleware, which was also used to parse and validate both the original and the hybrid messages. Both versions of the data instance (one pure XML, one embedded in the HL7v2 message) were equally validated and the RDF-based semantics recovered by the receiving side of the prototype from the shared XML schema. This study demonstrated the semantic enrichment of HL7v2 messages for intensive-software telemedicine systems for trauma care, by validating components of extracts generated in various computing environments. The adoption of the method proposed in this study ensures the compliance of the HL7v2 standard in Semantic Web technologies.

Addressing the Challenges of Multi-Domain Data Integration with the SemantEco Framework

NASA Astrophysics Data System (ADS)

Patton, E. W.; Seyed, P.; McGuinness, D. L.

2013-12-01

Data integration across multiple domains will continue to be a challenge with the proliferation of big data in the sciences. Data origination issues and how data are manipulated are critical to enable scientists to understand and consume disparate datasets as research becomes more multidisciplinary. We present the SemantEco framework as an exemplar for designing an integrative portal for data discovery, exploration, and interpretation that uses best practice W3C Recommendations. We use the Resource Description Framework (RDF) with extensible ontologies described in the Web Ontology Language (OWL) to provide graph-based data representation. Furthermore, SemantEco ingests data via the software package csv2rdf4lod, which generates data provenance using the W3C provenance recommendation (PROV). Our presentation will discuss benefits and challenges of semantic integration, their effect on runtime performance, and how the SemantEco framework assisted in identifying performance issues and improved query performance across multiple domains by an order of magnitude. SemantEco benefits from a semantic approach that provides an 'open world', which allows data to incrementally change just as it does in the real world. SemantEco modules may load new ontologies and data using the W3C's SPARQL Protocol and RDF Query Language via HTTP. Modules may also provide user interface elements for applications and query capabilities to support new use cases. Modules can associate with domains, which are first-class objects in SemantEco. This enables SemantEco to perform integration and reasoning both within and across domains on module-provided data. The SemantEco framework has been used to construct a web portal for environmental and ecological data. The portal includes water and air quality data from the U.S. Geological Survey (USGS) and Environmental Protection Agency (EPA) and species observation counts for birds and fish from the Avian Knowledge Network and the Santa Barbara Long Term Ecological Research, respectively. We provide regulation ontologies using OWL2 datatype facets to detect out-of-range measurements for environmental standards set by the EPA, i.a. Users adjust queries using module-defined facets and a map presents the resulting measurement sites. Custom icons identify sites that violate regulations, making them easy to locate. Selecting a site gives the option of charting spatially proximate data from different domains over time. Our portal currently provides 1.6 billion triples of scientific data in RDF. We segment data by ZIP code and reasoning over 2157 measurements with our EPA regulation ontology that contains 131 regulations takes 2.5 seconds on a 2.4 GHz Intel Core 2 Quad with 8 GB of RAM. SemantEco's modular design and reasoning capabilities make it an exemplar for building multidisciplinary data integration tools that provide data access to scientists and the general population alike. Its provenance tracking provides accountability and its reasoning services can assist users in interpreting data. Future work includes support for geographical queries using the Open Geospatial Consortium's GeoSPARQL standard.

Knowledge bases built on web languages from the point of view of predicate logics

NASA Astrophysics Data System (ADS)

Vajgl, Marek; Lukasová, Alena; Žáček, Martin

2017-06-01

The article undergoes evaluation of formal systems created on the base of web (ontology/concept) languages by simplifying the usual approach of knowledge representation within the FOPL, but sharing its expressiveness, semantic correct-ness, completeness and decidability. Evaluation of two of them - that one based on description logic and that one built on RDF model principles - identifies some of the lacks of those formal systems and presents, if possible, corrections of them. Possibilities to build an inference system capable to obtain new further knowledge over given knowledge bases including those describing domains by giant linked domain databases has been taken into account. Moreover, the directions towards simplifying FOPL language discussed here has been evaluated from the point of view of a possibility to become a web language for fulfilling an idea of semantic web.

Organizing Diverse, Distributed Project Information

NASA Technical Reports Server (NTRS)

Keller, Richard M.

2003-01-01

SemanticOrganizer is a software application designed to organize and integrate information generated within a distributed organization or as part of a project that involves multiple, geographically dispersed collaborators. SemanticOrganizer incorporates the capabilities of database storage, document sharing, hypermedia navigation, and semantic-interlinking into a system that can be customized to satisfy the specific information-management needs of different user communities. The program provides a centralized repository of information that is both secure and accessible to project collaborators via the World Wide Web. SemanticOrganizer's repository can be used to collect diverse information (including forms, documents, notes, data, spreadsheets, images, and sounds) from computers at collaborators work sites. The program organizes the information using a unique network-structured conceptual framework, wherein each node represents a data record that contains not only the original information but also metadata (in effect, standardized data that characterize the information). Links among nodes express semantic relationships among the data records. The program features a Web interface through which users enter, interlink, and/or search for information in the repository. By use of this repository, the collaborators have immediate access to the most recent project information, as well as to archived information. A key advantage to SemanticOrganizer is its ability to interlink information together in a natural fashion using customized terminology and concepts that are familiar to a user community.

Extending the GI Brokering Suite to Support New Interoperability Specifications

NASA Astrophysics Data System (ADS)

Boldrini, E.; Papeschi, F.; Santoro, M.; Nativi, S.

2014-12-01

The GI brokering suite provides the discovery, access, and semantic Brokers (i.e. GI-cat, GI-axe, GI-sem) that empower a Brokering framework for multi-disciplinary and multi-organizational interoperability. GI suite has been successfully deployed in the framework of several programmes and initiatives, such as European Union funded projects, NSF BCube, and the intergovernmental coordinated effort Global Earth Observation System of Systems (GEOSS). Each GI suite Broker facilitates interoperability for a particular functionality (i.e. discovery, access, semantic extension) among a set of brokered resources published by autonomous providers (e.g. data repositories, web services, semantic assets) and a set of heterogeneous consumers (e.g. client applications, portals, apps). A wide set of data models, encoding formats, and service protocols are already supported by the GI suite, such as the ones defined by international standardizing organizations like OGC and ISO (e.g. WxS, CSW, SWE, GML, netCDF) and by Community specifications (e.g. THREDDS, OpenSearch, OPeNDAP, ESRI APIs). Using GI suite, resources published by a particular Community or organization through their specific technology (e.g. OPeNDAP/netCDF) can be transparently discovered, accessed, and used by different Communities utilizing their preferred tools (e.g. a GIS visualizing WMS layers). Since Information Technology is a moving target, new standards and technologies continuously emerge and are adopted in the Earth Science context too. Therefore, GI Brokering suite was conceived to be flexible and accommodate new interoperability protocols and data models. For example, GI suite has recently added support to well-used specifications, introduced to implement Linked data, Semantic Web and precise community needs. Amongst the others, they included: DCAT: a RDF vocabulary designed to facilitate interoperability between Web data catalogs. CKAN: a data management system for data distribution, particularly used by public administrations. CERIF: used by CRIS (Current Research Information System) instances. HYRAX Server: a scientific dataset publishing component. This presentation will discuss these and other latest GI suite extensions implemented to support new interoperability protocols in use by the Earth Science Communities.

NeuroRDF: semantic integration of highly curated data to prioritize biomarker candidates in Alzheimer's disease.

PubMed

Iyappan, Anandhi; Kawalia, Shweta Bagewadi; Raschka, Tamara; Hofmann-Apitius, Martin; Senger, Philipp

2016-07-08

Neurodegenerative diseases are incurable and debilitating indications with huge social and economic impact, where much is still to be learnt about the underlying molecular events. Mechanistic disease models could offer a knowledge framework to help decipher the complex interactions that occur at molecular and cellular levels. This motivates the need for the development of an approach integrating highly curated and heterogeneous data into a disease model of different regulatory data layers. Although several disease models exist, they often do not consider the quality of underlying data. Moreover, even with the current advancements in semantic web technology, we still do not have cure for complex diseases like Alzheimer's disease. One of the key reasons accountable for this could be the increasing gap between generated data and the derived knowledge. In this paper, we describe an approach, called as NeuroRDF, to develop an integrative framework for modeling curated knowledge in the area of complex neurodegenerative diseases. The core of this strategy lies in the usage of well curated and context specific data for integration into one single semantic web-based framework, RDF. This increases the probability of the derived knowledge to be novel and reliable in a specific disease context. This infrastructure integrates highly curated data from databases (Bind, IntAct, etc.), literature (PubMed), and gene expression resources (such as GEO and ArrayExpress). We illustrate the effectiveness of our approach by asking real-world biomedical questions that link these resources to prioritize the plausible biomarker candidates. Among the 13 prioritized candidate genes, we identified MIF to be a potential emerging candidate due to its role as a pro-inflammatory cytokine. We additionally report on the effort and challenges faced during generation of such an indication-specific knowledge base comprising of curated and quality-controlled data. Although many alternative approaches have been proposed and practiced for modeling diseases, the semantic web technology is a flexible and well established solution for harmonized aggregation. The benefit of this work, to use high quality and context specific data, becomes apparent in speculating previously unattended biomarker candidates around a well-known mechanism, further leveraged for experimental investigations.

Semantically Interoperable XML Data

PubMed Central

Vergara-Niedermayr, Cristobal; Wang, Fusheng; Pan, Tony; Kurc, Tahsin; Saltz, Joel

2013-01-01

XML is ubiquitously used as an information exchange platform for web-based applications in healthcare, life sciences, and many other domains. Proliferating XML data are now managed through latest native XML database technologies. XML data sources conforming to common XML schemas could be shared and integrated with syntactic interoperability. Semantic interoperability can be achieved through semantic annotations of data models using common data elements linked to concepts from ontologies. In this paper, we present a framework and software system to support the development of semantic interoperable XML based data sources that can be shared through a Grid infrastructure. We also present our work on supporting semantic validated XML data through semantic annotations for XML Schema, semantic validation and semantic authoring of XML data. We demonstrate the use of the system for a biomedical database of medical image annotations and markups. PMID:25298789

JournalMap: Geo-semantic searching for relevant knowledge

USDA-ARS?s Scientific Manuscript database

Ecologists struggling to understand rapidly changing environments and evolving ecosystem threats need quick access to relevant research and documentation of natural systems. The advent of semantic and aggregation searching (e.g., Google Scholar, Web of Science) has made it easier to find useful lite...

Constructive Ontology Engineering

ERIC Educational Resources Information Center

Sousan, William L.

2010-01-01

The proliferation of the Semantic Web depends on ontologies for knowledge sharing, semantic annotation, data fusion, and descriptions of data for machine interpretation. However, ontologies are difficult to create and maintain. In addition, their structure and content may vary depending on the application and domain. Several methods described in…

Interoperability in Personalized Adaptive Learning

ERIC Educational Resources Information Center

Aroyo, Lora; Dolog, Peter; Houben, Geert-Jan; Kravcik, Milos; Naeve, Ambjorn; Nilsson, Mikael; Wild, Fridolin

2006-01-01

Personalized adaptive learning requires semantic-based and context-aware systems to manage the Web knowledge efficiently as well as to achieve semantic interoperability between heterogeneous information resources and services. The technological and conceptual differences can be bridged either by means of standards or via approaches based on the…

OpenFlyData: an exemplar data web integrating gene expression data on the fruit fly Drosophila melanogaster.

PubMed

Miles, Alistair; Zhao, Jun; Klyne, Graham; White-Cooper, Helen; Shotton, David

2010-10-01

Integrating heterogeneous data across distributed sources is a major requirement for in silico bioinformatics supporting translational research. For example, genome-scale data on patterns of gene expression in the fruit fly Drosophila melanogaster are widely used in functional genomic studies in many organisms to inform candidate gene selection and validate experimental results. However, current data integration solutions tend to be heavy weight, and require significant initial and ongoing investment of effort. Development of a common Web-based data integration infrastructure (a.k.a. data web), using Semantic Web standards, promises to alleviate these difficulties, but little is known about the feasibility, costs, risks or practical means of migrating to such an infrastructure. We describe the development of OpenFlyData, a proof-of-concept system integrating gene expression data on D. melanogaster, combining Semantic Web standards with light-weight approaches to Web programming based on Web 2.0 design patterns. To support researchers designing and validating functional genomic studies, OpenFlyData includes user-facing search applications providing intuitive access to and comparison of gene expression data from FlyAtlas, the BDGP in situ database, and FlyTED, using data from FlyBase to expand and disambiguate gene names. OpenFlyData's services are also openly accessible, and are available for reuse by other bioinformaticians and application developers. Semi-automated methods and tools were developed to support labour- and knowledge-intensive tasks involved in deploying SPARQL services. These include methods for generating ontologies and relational-to-RDF mappings for relational databases, which we illustrate using the FlyBase Chado database schema; and methods for mapping gene identifiers between databases. The advantages of using Semantic Web standards for biomedical data integration are discussed, as are open issues. In particular, although the performance of open source SPARQL implementations is sufficient to query gene expression data directly from user-facing applications such as Web-based data fusions (a.k.a. mashups), we found open SPARQL endpoints to be vulnerable to denial-of-service-type problems, which must be mitigated to ensure reliability of services based on this standard. These results are relevant to data integration activities in translational bioinformatics. The gene expression search applications and SPARQL endpoints developed for OpenFlyData are deployed at http://openflydata.org. FlyUI, a library of JavaScript widgets providing re-usable user-interface components for Drosophila gene expression data, is available at http://flyui.googlecode.com. Software and ontologies to support transformation of data from FlyBase, FlyAtlas, BDGP and FlyTED to RDF are available at http://openflydata.googlecode.com. SPARQLite, an implementation of the SPARQL protocol, is available at http://sparqlite.googlecode.com. All software is provided under the GPL version 3 open source license.

Semantic Enhancement for Enterprise Data Management

NASA Astrophysics Data System (ADS)

Ma, Li; Sun, Xingzhi; Cao, Feng; Wang, Chen; Wang, Xiaoyuan; Kanellos, Nick; Wolfson, Dan; Pan, Yue

Taking customer data as an example, the paper presents an approach to enhance the management of enterprise data by using Semantic Web technologies. Customer data is the most important kind of core business entity a company uses repeatedly across many business processes and systems, and customer data management (CDM) is becoming critical for enterprises because it keeps a single, complete and accurate record of customers across the enterprise. Existing CDM systems focus on integrating customer data from all customer-facing channels and front and back office systems through multiple interfaces, as well as publishing customer data to different applications. To make the effective use of the CDM system, this paper investigates semantic query and analysis over the integrated and centralized customer data, enabling automatic classification and relationship discovery. We have implemented these features over IBM Websphere Customer Center, and shown the prototype to our clients. We believe that our study and experiences are valuable for both Semantic Web community and data management community.

BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains

PubMed Central

2014-01-01

The application of semantic technologies to the integration of biological data and the interoperability of bioinformatics analysis and visualization tools has been the common theme of a series of annual BioHackathons hosted in Japan for the past five years. Here we provide a review of the activities and outcomes from the BioHackathons held in 2011 in Kyoto and 2012 in Toyama. In order to efficiently implement semantic technologies in the life sciences, participants formed various sub-groups and worked on the following topics: Resource Description Framework (RDF) models for specific domains, text mining of the literature, ontology development, essential metadata for biological databases, platforms to enable efficient Semantic Web technology development and interoperability, and the development of applications for Semantic Web data. In this review, we briefly introduce the themes covered by these sub-groups. The observations made, conclusions drawn, and software development projects that emerged from these activities are discussed. PMID:24495517

Query Results Clustering by Extending SPARQL with CLUSTER BY

NASA Astrophysics Data System (ADS)

Ławrynowicz, Agnieszka

The task of dynamic clustering of the search results proved to be useful in the Web context, where the user often does not know the granularity of the search results in advance. The goal of this paper is to provide a declarative way for invoking dynamic clustering of the results of queries submitted over Semantic Web data. To achieve this goal the paper proposes an approach that extends SPARQL by clustering abilities. The approach introduces a new statement, CLUSTER BY, into the SPARQL grammar and proposes semantics for such extension.

Towards a Semantic Web of Community, Content and Interactions

DTIC Science & Technology

2005-09-01

importance of setting goals and deadlines as a means to achieving progress on the nebulous road to a dissertation. Jim Herbsleb sparked my interest in...RDF, such as Turtle [Bec04], a text syntax for RDF, and N-Triples [GDB04]. 45 </dc:creator> <dc:title>The Semantic Web: An Introduction</dc:title...2):22–41, 1990. 2.2.2 [Bec04] Dave Beckett. Turtle –terse rdf triple language. http://www.ilrt.bris.ac.uk/discovery/2004/01/ turtle /, January 2004. 4

Contextual advertisement placement in printed media

NASA Astrophysics Data System (ADS)

Liu, Sam; Joshi, Parag

2010-02-01

Advertisements today provide the necessary revenue model supporting the WWW ecosystem. Targeted or contextual ad insertion plays an important role in optimizing the financial return of this model. Nearly all the current ads that appear on web sites are geared for display purposes such as banner and "pay-per-click". Little attention, however, is focused on deriving additional ad revenues when the content is repurposed for alternative mean of presentation, e.g. being printed. Although more and more content is moving to the Web, there are still many occasions where printed output of web content is desirable, such as maps and articles; thus printed ad insertion can potentially be lucrative. In this paper, we describe a contextual ad insertion network aimed to realize new revenue for print service providers for web printing. We introduce a cloud print service that enables contextual ads insertion, with respect to the main web page content, when a printout of the page is requested. To encourage service utilization, it would provide higher quality printouts than what is possible from current browser print drivers, which generally produce poor outputs, e.g. ill formatted pages. At this juncture we will limit the scope to only article-related web pages although the concept can be extended to arbitrary web pages. The key components of this system include (1) the extraction of article from web pages, (2) the extraction of semantics from article, (3) querying the ad database for matching advertisement or coupon, and (4) joint content and ad layout for print outputs.

Analysis and visualization of disease courses in a semantically-enabled cancer registry.

PubMed

Esteban-Gil, Angel; Fernández-Breis, Jesualdo Tomás; Boeker, Martin

2017-09-29

Regional and epidemiological cancer registries are important for cancer research and the quality management of cancer treatment. Many technological solutions are available to collect and analyse data for cancer registries nowadays. However, the lack of a well-defined common semantic model is a problem when user-defined analyses and data linking to external resources are required. The objectives of this study are: (1) design of a semantic model for local cancer registries; (2) development of a semantically-enabled cancer registry based on this model; and (3) semantic exploitation of the cancer registry for analysing and visualising disease courses. Our proposal is based on our previous results and experience working with semantic technologies. Data stored in a cancer registry database were transformed into RDF employing a process driven by OWL ontologies. The semantic representation of the data was then processed to extract semantic patient profiles, which were exploited by means of SPARQL queries to identify groups of similar patients and to analyse the disease timelines of patients. Based on the requirements analysis, we have produced a draft of an ontology that models the semantics of a local cancer registry in a pragmatic extensible way. We have implemented a Semantic Web platform that allows transforming and storing data from cancer registries in RDF. This platform also permits users to formulate incremental user-defined queries through a graphical user interface. The query results can be displayed in several customisable ways. The complex disease timelines of individual patients can be clearly represented. Different events, e.g. different therapies and disease courses, are presented according to their temporal and causal relations. The presented platform is an example of the parallel development of ontologies and applications that take advantage of semantic web technologies in the medical field. The semantic structure of the representation renders it easy to analyse key figures of the patients and their evolution at different granularity levels.

The OceanLink Project

NASA Astrophysics Data System (ADS)

Narock, T.; Arko, R. A.; Carbotte, S. M.; Chandler, C. L.; Cheatham, M.; Finin, T.; Hitzler, P.; Krisnadhi, A.; Raymond, L. M.; Shepherd, A.; Wiebe, P. H.

2014-12-01

A wide spectrum of maturing methods and tools, collectively characterized as the Semantic Web, is helping to vastly improve the dissemination of scientific research. Creating semantic integration requires input from both domain and cyberinfrastructure scientists. OceanLink, an NSF EarthCube Building Block, is demonstrating semantic technologies through the integration of geoscience data repositories, library holdings, conference abstracts, and funded research awards. Meeting project objectives involves applying semantic technologies to support data representation, discovery, sharing and integration. Our semantic cyberinfrastructure components include ontology design patterns, Linked Data collections, semantic provenance, and associated services to enhance data and knowledge discovery, interoperation, and integration. We discuss how these components are integrated, the continued automated and semi-automated creation of semantic metadata, and techniques we have developed to integrate ontologies, link resources, and preserve provenance and attribution.

Applying semantic web technologies for phenome-wide scan using an electronic health record linked Biobank

PubMed Central

2012-01-01

Background The ability to conduct genome-wide association studies (GWAS) has enabled new exploration of how genetic variations contribute to health and disease etiology. However, historically GWAS have been limited by inadequate sample size due to associated costs for genotyping and phenotyping of study subjects. This has prompted several academic medical centers to form “biobanks” where biospecimens linked to personal health information, typically in electronic health records (EHRs), are collected and stored on a large number of subjects. This provides tremendous opportunities to discover novel genotype-phenotype associations and foster hypotheses generation. Results In this work, we study how emerging Semantic Web technologies can be applied in conjunction with clinical and genotype data stored at the Mayo Clinic Biobank to mine the phenotype data for genetic associations. In particular, we demonstrate the role of using Resource Description Framework (RDF) for representing EHR diagnoses and procedure data, and enable federated querying via standardized Web protocols to identify subjects genotyped for Type 2 Diabetes and Hypothyroidism to discover gene-disease associations. Our study highlights the potential of Web-scale data federation techniques to execute complex queries. Conclusions This study demonstrates how Semantic Web technologies can be applied in conjunction with clinical data stored in EHRs to accurately identify subjects with specific diseases and phenotypes, and identify genotype-phenotype associations. PMID:23244446

Semantic markup of sensor capabilities: how simple it too simple?

NASA Astrophysics Data System (ADS)

Rueda-Velasquez, C. A.; Janowicz, K.; Fredericks, J.

2016-12-01

Semantics plays a key role for the publication, retrieval, integration, and reuse of observational data across the geosciences. In most cases, one can safely assume that the providers of such data, e.g., individual scientists, understand the observation context in which their data are collected,e.g., the used observation procedure, the sampling strategy, the feature of interest being studied, and so forth. However, can we expect that the same is true for the technical details of the used sensors and especially the nuanced changes that can impact observations in often unpredictable ways? Should the burden of annotating the sensor capabilities, firmware, operation ranges, and so forth be really part of a scientist's responsibility? Ideally, semantic annotations should be provided by the parties that understand these details and have a vested interest in maintaining these data. With manufactures providing semantically-enabled metadata for their sensors and instruments, observations could more easily be annotated and thereby enriched using this information. Unfortunately, today's sensor ontologies and tool chains developed for the Semantic Web community require expertise beyond the knowledge and interest of most manufacturers. Consequently, knowledge engineers need to better understand the sweet spot between simple ontologies/vocabularies and sufficient expressivity as well as the tools required to enable manufacturers to share data about their sensors. Here, we report on the current results of EarthCube's X-Domes project that aims to address the questions outlined above.

Semantic Services in e-Learning: An Argumentation Case Study

ERIC Educational Resources Information Center

Moreale, Emanuela; Vargas-Vera, Maria

2004-01-01

This paper outlines an e-Learning services architecture offering semantic-based services to students and tutors, in particular ways to browse and obtain information through web services. Services could include registration, authentication, tutoring systems, smart question answering for students' queries, automated marking systems and a student…

Auto-Relevancy Baseline: A Hybrid System Without Human Feedback

DTIC Science & Technology

2010-11-01

classical Bayes algorithm upon the pseudo-hybridization of SemanticA and Latent Semantic IndexingBC systems should smooth out historically high yet...black box emulated a machine learning topic expert. Similar to some Web methods, the initial topics within the legal document were expanded upon

Developing Visualization Techniques for Semantics-based Information Networks

NASA Technical Reports Server (NTRS)

Keller, Richard M.; Hall, David R.

2003-01-01

Information systems incorporating complex network structured information spaces with a semantic underpinning - such as hypermedia networks, semantic networks, topic maps, and concept maps - are being deployed to solve some of NASA s critical information management problems. This paper describes some of the human interaction and navigation problems associated with complex semantic information spaces and describes a set of new visual interface approaches to address these problems. A key strategy is to leverage semantic knowledge represented within these information spaces to construct abstractions and views that will be meaningful to the human user. Human-computer interaction methodologies will guide the development and evaluation of these approaches, which will benefit deployed NASA systems and also apply to information systems based on the emerging Semantic Web.

Dynamic Generation of Reduced Ontologies to Support Resource Constraints of Mobile Devices

ERIC Educational Resources Information Center

Schrimpsher, Dan

2011-01-01

As Web Services and the Semantic Web become more important, enabling technologies such as web service ontologies will grow larger. At the same time, use of mobile devices to access web services has doubled in the last year. The ability of these resource constrained devices to download and reason across these ontologies to support service discovery…

Knowledge Provenance in Semantic Wikis

NASA Astrophysics Data System (ADS)

Ding, L.; Bao, J.; McGuinness, D. L.

2008-12-01

Collaborative online environments with a technical Wiki infrastructure are becoming more widespread. One of the strengths of a Wiki environment is that it is relatively easy for numerous users to contribute original content and modify existing content (potentially originally generated by others). As more users begin to depend on informational content that is evolving by Wiki communities, it becomes more important to track the provenance of the information. Semantic Wikis expand upon traditional Wiki environments by adding some computationally understandable encodings of some of the terms and relationships in Wikis. We have developed a semantic Wiki environment that expands a semantic Wiki with provenance markup. Provenance of original contributions as well as modifications is encoded using the provenance markup component of the Proof Markup Language. The Wiki environment provides the provenance markup automatically, thus users are not required to make specific encodings of author, contribution date, and modification trail. Further, our Wiki environment includes a search component that understands the provenance primitives and thus can be used to provide a provenance-aware search facility. We will describe the knowledge provenance infrastructure of our Semantic Wiki and show how it is being used as the foundation of our group web site as well as a number of project web sites.

Semantic Integration for Marine Science Interoperability Using Web Technologies

NASA Astrophysics Data System (ADS)

Rueda, C.; Bermudez, L.; Graybeal, J.; Isenor, A. W.

2008-12-01

The Marine Metadata Interoperability Project, MMI (http://marinemetadata.org) promotes the exchange, integration, and use of marine data through enhanced data publishing, discovery, documentation, and accessibility. A key effort is the definition of an Architectural Framework and Operational Concept for Semantic Interoperability (http://marinemetadata.org/sfc), which is complemented with the development of tools that realize critical use cases in semantic interoperability. In this presentation, we describe a set of such Semantic Web tools that allow performing important interoperability tasks, ranging from the creation of controlled vocabularies and the mapping of terms across multiple ontologies, to the online registration, storage, and search services needed to work with the ontologies (http://mmisw.org). This set of services uses Web standards and technologies, including Resource Description Framework (RDF), Web Ontology language (OWL), Web services, and toolkits for Rich Internet Application development. We will describe the following components: MMI Ontology Registry: The MMI Ontology Registry and Repository provides registry and storage services for ontologies. Entries in the registry are associated with projects defined by the registered users. Also, sophisticated search functions, for example according to metadata items and vocabulary terms, are provided. Client applications can submit search requests using the WC3 SPARQL Query Language for RDF. Voc2RDF: This component converts an ASCII comma-delimited set of terms and definitions into an RDF file. Voc2RDF facilitates the creation of controlled vocabularies by using a simple form-based user interface. Created vocabularies and their descriptive metadata can be submitted to the MMI Ontology Registry for versioning and community access. VINE: The Vocabulary Integration Environment component allows the user to map vocabulary terms across multiple ontologies. Various relationships can be established, for example exactMatch, narrowerThan, and subClassOf. VINE can compute inferred mappings based on the given associations. Attributes about each mapping, like comments and a confidence level, can also be included. VINE also supports registering and storing resulting mapping files in the Ontology Registry. The presentation will describe the application of semantic technologies in general, and our planned applications in particular, to solve data management problems in the marine and environmental sciences.

ODMedit: uniform semantic annotation for data integration in medicine based on a public metadata repository.

PubMed

Dugas, Martin; Meidt, Alexandra; Neuhaus, Philipp; Storck, Michael; Varghese, Julian

2016-06-01

The volume and complexity of patient data - especially in personalised medicine - is steadily increasing, both regarding clinical data and genomic profiles: Typically more than 1,000 items (e.g., laboratory values, vital signs, diagnostic tests etc.) are collected per patient in clinical trials. In oncology hundreds of mutations can potentially be detected for each patient by genomic profiling. Therefore data integration from multiple sources constitutes a key challenge for medical research and healthcare. Semantic annotation of data elements can facilitate to identify matching data elements in different sources and thereby supports data integration. Millions of different annotations are required due to the semantic richness of patient data. These annotations should be uniform, i.e., two matching data elements shall contain the same annotations. However, large terminologies like SNOMED CT or UMLS don't provide uniform coding. It is proposed to develop semantic annotations of medical data elements based on a large-scale public metadata repository. To achieve uniform codes, semantic annotations shall be re-used if a matching data element is available in the metadata repository. A web-based tool called ODMedit ( https://odmeditor.uni-muenster.de/ ) was developed to create data models with uniform semantic annotations. It contains ~800,000 terms with semantic annotations which were derived from ~5,800 models from the portal of medical data models (MDM). The tool was successfully applied to manually annotate 22 forms with 292 data items from CDISC and to update 1,495 data models of the MDM portal. Uniform manual semantic annotation of data models is feasible in principle, but requires a large-scale collaborative effort due to the semantic richness of patient data. A web-based tool for these annotations is available, which is linked to a public metadata repository.

Opportunities for the Mashup of Heterogenous Data Server via Semantic Web Technology

NASA Astrophysics Data System (ADS)

Ritschel, Bernd; Seelus, Christoph; Neher, Günther; Iyemori, Toshihiko; Koyama, Yukinobu; Yatagai, Akiyo; Murayama, Yasuhiro; King, Todd; Hughes, John; Fung, Shing; Galkin, Ivan; Hapgood, Michael; Belehaki, Anna

2015-04-01

Opportunities for the Mashup of Heterogenous Data Server via Semantic Web Technology European Union ESPAS, Japanese IUGONET and GFZ ISDC data server are developed for the ingestion, archiving and distributing of geo and space science domain data. Main parts of the data -managed by the mentioned data server- are related to near earth-space and geomagnetic field data. A smart mashup of the data server would allow a seamless browse and access to data and related context information. However the achievement of a high level of interoperability is a challenge because the data server are based on different data models and software frameworks. This paper is focused on the latest experiments and results for the mashup of the data server using the semantic Web approach. Besides the mashup of domain and terminological ontologies, especially the options to connect data managed by relational databases using D2R server and SPARQL technology will be addressed. A successful realization of the data server mashup will not only have a positive impact to the data users of the specific scientific domain but also to related projects, such as e.g. the development of a new interoperable version of NASA's Planetary Data System (PDS) or ICUS's World Data System alliance. ESPAS data server: https://www.espas-fp7.eu/portal/ IUGONET data server: http://search.iugonet.org/iugonet/ GFZ ISDC data server (semantic Web based prototype): http://rz-vm30.gfz-potsdam.de/drupal-7.9/ NASA PDS: http://pds.nasa.gov ICSU-WDS: https://www.icsu-wds.org

tOWL: a temporal Web Ontology Language.

PubMed

Milea, Viorel; Frasincar, Flavius; Kaymak, Uzay

2012-02-01

Through its interoperability and reasoning capabilities, the Semantic Web opens a realm of possibilities for developing intelligent systems on the Web. The Web Ontology Language (OWL) is the most expressive standard language for modeling ontologies, the cornerstone of the Semantic Web. However, up until now, no standard way of expressing time and time-dependent information in OWL has been provided. In this paper, we present a temporal extension of the very expressive fragment SHIN(D) of the OWL Description Logic language, resulting in the temporal OWL language. Through a layered approach, we introduce three extensions: 1) concrete domains, which allow the representation of restrictions using concrete domain binary predicates; 2) temporal representation , which introduces time points, relations between time points, intervals, and Allen's 13 interval relations into the language; and 3) timeslices/fluents, which implement a perdurantist view on individuals and allow for the representation of complex temporal aspects, such as process state transitions. We illustrate the expressiveness of the newly introduced language by using an example from the financial domain.

Convergence of Health Level Seven Version 2 Messages to Semantic Web Technologies for Software-Intensive Systems in Telemedicine Trauma Care

PubMed Central

Cook, Timothy Wayne; Cavalini, Luciana Tricai

2016-01-01

Objectives To present the technical background and the development of a procedure that enriches the semantics of Health Level Seven version 2 (HL7v2) messages for software-intensive systems in telemedicine trauma care. Methods This study followed a multilevel model-driven approach for the development of semantically interoperable health information systems. The Pre-Hospital Trauma Life Support (PHTLS) ABCDE protocol was adopted as the use case. A prototype application embedded the semantics into an HL7v2 message as an eXtensible Markup Language (XML) file, which was validated against an XML schema that defines constraints on a common reference model. This message was exchanged with a second prototype application, developed on the Mirth middleware, which was also used to parse and validate both the original and the hybrid messages. Results Both versions of the data instance (one pure XML, one embedded in the HL7v2 message) were equally validated and the RDF-based semantics recovered by the receiving side of the prototype from the shared XML schema. Conclusions This study demonstrated the semantic enrichment of HL7v2 messages for intensive-software telemedicine systems for trauma care, by validating components of extracts generated in various computing environments. The adoption of the method proposed in this study ensures the compliance of the HL7v2 standard in Semantic Web technologies. PMID:26893947

Semantic Web Service Delivery in Healthcare Based on Functional and Non-Functional Properties.

PubMed

Schweitzer, Marco; Gorfer, Thilo; Hörbst, Alexander

2017-01-01

In the past decades, a lot of endeavor has been made on the trans-institutional exchange of healthcare data through electronic health records (EHR) in order to obtain a lifelong, shared accessible health record of a patient. Besides basic information exchange, there is a growing need for Information and Communication Technology (ICT) to support the use of the collected health data in an individual, case-specific workflow-based manner. This paper presents the results on how workflows can be used to process data from electronic health records, following a semantic web service approach that enables automatic discovery, composition and invocation of suitable web services. Based on this solution, the user (physician) can define its needs from a domain-specific perspective, whereas the ICT-system fulfills those needs with modular web services. By involving also non-functional properties for the service selection, this approach is even more suitable for the dynamic medical domain.

E-Learning for Depth in the Semantic Web

ERIC Educational Resources Information Center

Shafrir, Uri; Etkind, Masha

2006-01-01

In this paper, we describe concept parsing algorithms, a novel semantic analysis methodology at the core of a new pedagogy that focuses learners attention on deep comprehension of the conceptual content of learned material. Two new e-learning tools are described in some detail: interactive concept discovery learning and meaning equivalence…

Towards Text Copyright Detection Using Metadata in Web Applications

ERIC Educational Resources Information Center

Poulos, Marios; Korfiatis, Nikolaos; Bokos, George

2011-01-01

Purpose: This paper aims to present the semantic content identifier (SCI), a permanent identifier, computed through a linear-time onion-peeling algorithm that enables the extraction of semantic features from a text, and the integration of this information within the permanent identifier. Design/methodology/approach: The authors employ SCI to…

Virtual Field Sites: Losses and Gains in Authenticity with Semantic Technologies

ERIC Educational Resources Information Center

Litherland, Kate; Stott, Tim A.

2012-01-01

The authors investigate the potential of semantic web technologies to enhance "Virtual Fieldwork" resources and learning activities in the Geosciences. They consider the difficulties inherent in the concept of Virtual Fieldwork and how these might be reconciled with the desire to provide students with "authentic" tools for…

Focused Belief Measures for Uncertainty Quantification in High Performance Semantic Analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Joslyn, Cliff A.; Weaver, Jesse R.

In web-scale semantic data analytics there is a great need for methods which aggregate uncertainty claims, on the one hand respecting the information provided as accurately as possible, while on the other still being tractable. Traditional statistical methods are more robust, but only represent distributional, additive uncertainty. Generalized information theory methods, including fuzzy systems and Dempster-Shafer (DS) evidence theory, represent multiple forms of uncertainty, but are computationally and methodologically difficult. We require methods which provide an effective balance between the complete representation of the full complexity of uncertainty claims in their interaction, while satisfying the needs of both computational complexitymore » and human cognition. Here we build on J{\\o}sang's subjective logic to posit methods in focused belief measures (FBMs), where a full DS structure is focused to a single event. The resulting ternary logical structure is posited to be able to capture the minimal amount of generalized complexity needed at a maximum of computational efficiency. We demonstrate the efficacy of this approach in a web ingest experiment over the 2012 Billion Triple dataset from the Semantic Web Challenge.« less

Semantic orchestration of image processing services for environmental analysis

NASA Astrophysics Data System (ADS)

Ranisavljević, Élisabeth; Devin, Florent; Laffly, Dominique; Le Nir, Yannick

2013-09-01

In order to analyze environmental dynamics, a major process is the classification of the different phenomena of the site (e.g. ice and snow for a glacier). When using in situ pictures, this classification requires data pre-processing. Not all the pictures need the same sequence of processes depending on the disturbances. Until now, these sequences have been done manually, which restricts the processing of large amount of data. In this paper, we present how to realize a semantic orchestration to automate the sequencing for the analysis. It combines two advantages: solving the problem of the amount of processing, and diversifying the possibilities in the data processing. We define a BPEL description to express the sequences. This BPEL uses some web services to run the data processing. Each web service is semantically annotated using an ontology of image processing. The dynamic modification of the BPEL is done using SPARQL queries on these annotated web services. The results obtained by a prototype implementing this method validate the construction of the different workflows that can be applied to a large number of pictures.

Building a knowledge base of severe adverse drug events based on AERS reporting data using semantic web technologies.

PubMed

Jiang, Guoqian; Wang, Liwei; Liu, Hongfang; Solbrig, Harold R; Chute, Christopher G

2013-01-01

A semantically coded knowledge base of adverse drug events (ADEs) with severity information is critical for clinical decision support systems and translational research applications. However it remains challenging to measure and identify the severity information of ADEs. The objective of the study is to develop and evaluate a semantic web based approach for building a knowledge base of severe ADEs based on the FDA Adverse Event Reporting System (AERS) reporting data. We utilized a normalized AERS reporting dataset and extracted putative drug-ADE pairs and their associated outcome codes in the domain of cardiac disorders. We validated the drug-ADE associations using ADE datasets from SIDe Effect Resource (SIDER) and the UMLS. We leveraged the Common Terminology Criteria for Adverse Event (CTCAE) grading system and classified the ADEs into the CTCAE in the Web Ontology Language (OWL). We identified and validated 2,444 unique Drug-ADE pairs in the domain of cardiac disorders, of which 760 pairs are in Grade 5, 775 pairs in Grade 4 and 2,196 pairs in Grade 3.

Digital Investigations of AN Archaeological Smart Point Cloud: a Real Time Web-Based Platform to Manage the Visualisation of Semantical Queries

NASA Astrophysics Data System (ADS)

Poux, F.; Neuville, R.; Hallot, P.; Van Wersch, L.; Luczfalvy Jancsó, A.; Billen, R.

2017-05-01

While virtual copies of the real world tend to be created faster than ever through point clouds and derivatives, their working proficiency by all professionals' demands adapted tools to facilitate knowledge dissemination. Digital investigations are changing the way cultural heritage researchers, archaeologists, and curators work and collaborate to progressively aggregate expertise through one common platform. In this paper, we present a web application in a WebGL framework accessible on any HTML5-compatible browser. It allows real time point cloud exploration of the mosaics in the Oratory of Germigny-des-Prés, and emphasises the ease of use as well as performances. Our reasoning engine is constructed over a semantically rich point cloud data structure, where metadata has been injected a priori. We developed a tool that directly allows semantic extraction and visualisation of pertinent information for the end users. It leads to efficient communication between actors by proposing optimal 3D viewpoints as a basis on which interactions can grow.

Perspectives for Electronic Books in the World Wide Web Age.

ERIC Educational Resources Information Center

Bry, Francois; Kraus, Michael

2002-01-01

Discusses the rapid growth of the World Wide Web and the lack of use of electronic books and suggests that specialized contents and device independence can make Web-based books compete with print. Topics include enhancing the hypertext model of XML; client-side adaptation, including browsers and navigation; and semantic modeling. (Author/LRW)

Towards the novel reasoning among particles in PSO by the use of RDF and SPARQL.

PubMed

Fister, Iztok; Yang, Xin-She; Ljubič, Karin; Fister, Dušan; Brest, Janez; Fister, Iztok

2014-01-01

The significant development of the Internet has posed some new challenges and many new programming tools have been developed to address such challenges. Today, semantic web is a modern paradigm for representing and accessing knowledge data on the Internet. This paper tries to use the semantic tools such as resource definition framework (RDF) and RDF query language (SPARQL) for the optimization purpose. These tools are combined with particle swarm optimization (PSO) and the selection of the best solutions depends on its fitness. Instead of the local best solution, a neighborhood of solutions for each particle can be defined and used for the calculation of the new position, based on the key ideas from semantic web domain. The preliminary results by optimizing ten benchmark functions showed the promising results and thus this method should be investigated further.

Live Social Semantics

NASA Astrophysics Data System (ADS)

Alani, Harith; Szomszor, Martin; Cattuto, Ciro; van den Broeck, Wouter; Correndo, Gianluca; Barrat, Alain

Social interactions are one of the key factors to the success of conferences and similar community gatherings. This paper describes a novel application that integrates data from the semantic web, online social networks, and a real-world contact sensing platform. This application was successfully deployed at ESWC09, and actively used by 139 people. Personal profiles of the participants were automatically generated using several Web 2.0 systems and semantic academic data sources, and integrated in real-time with face-to-face contact networks derived from wearable sensors. Integration of all these heterogeneous data layers made it possible to offer various services to conference attendees to enhance their social experience such as visualisation of contact data, and a site to explore and connect with other participants. This paper describes the architecture of the application, the services we provided, and the results we achieved in this deployment.

Solar-Terrestrial Ontology Development

NASA Astrophysics Data System (ADS)

McGuinness, D.; Fox, P.; Middleton, D.; Garcia, J.; Cinquni, L.; West, P.; Darnell, J. A.; Benedict, J.

2005-12-01

The development of an interdisciplinary virtual observatory (the Virtual Solar-Terrestrial Observatory; VSTO) as a scalable environment for searching, integrating, and analyzing databases distributed over the Internet requires a higher level of semantic interoperability than here-to-fore required by most (if not all) distributed data systems or discipline specific virtual observatories. The formalization of semantics using ontologies and their encodings for the internet (e.g. OWL - the Web Ontology Language), as well as the use of accompanying tools, such as reasoning, inference and explanation, open up both a substantial leap in options for interoperability and in the need for formal development principles to guide ontology development and use within modern, multi-tiered network data environments. In this presentation, we outline the formal methodologies we utilize in the VSTO project, the currently developed use-cases, ontologies and their relation to existing ontologies (such as SWEET).

Ontology-Based Exchange and Immediate Application of Business Calculation Definitions for Online Analytical Processing

NASA Astrophysics Data System (ADS)

Kehlenbeck, Matthias; Breitner, Michael H.

Business users define calculated facts based on the dimensions and facts contained in a data warehouse. These business calculation definitions contain necessary knowledge regarding quantitative relations for deep analyses and for the production of meaningful reports. The business calculation definitions are implementation and widely organization independent. But no automated procedures facilitating their exchange across organization and implementation boundaries exist. Separately each organization currently has to map its own business calculations to analysis and reporting tools. This paper presents an innovative approach based on standard Semantic Web technologies. This approach facilitates the exchange of business calculation definitions and allows for their automatic linking to specific data warehouses through semantic reasoning. A novel standard proxy server which enables the immediate application of exchanged definitions is introduced. Benefits of the approach are shown in a comprehensive case study.

Semantic Web-based digital, field and virtual geological

NASA Astrophysics Data System (ADS)

Babaie, H. A.

2012-12-01

Digital, field and virtual Semantic Web-based education (SWBE) of geological mapping requires the construction of a set of searchable, reusable, and interoperable digital learning objects (LO) for learners, teachers, and authors. These self-contained units of learning may be text, image, or audio, describing, for example, how to calculate the true dip of a layer from two structural contours or find the apparent dip along a line of section. A collection of multi-media LOs can be integrated, through domain and task ontologies, with mapping-related learning activities and Web services, for example, to search for the description of lithostratigraphic units in an area, or plotting orientation data on stereonet. Domain ontologies (e.g., GeologicStructure, Lithostratigraphy, Rock) represent knowledge in formal languages (RDF, OWL) by explicitly specifying concepts, relations, and theories involved in geological mapping. These ontologies are used by task ontologies that formalize the semantics of computational tasks (e.g., measuring the true thickness of a formation) and activities (e.g., construction of cross section) for all actors to solve specific problems (making map, instruction, learning support, authoring). A SWBE system for geological mapping should also involve ontologies to formalize teaching strategy (pedagogical styles), learner model (e.g., for student performance, personalization of learning), interface (entry points for activities of all actors), communication (exchange of messages among different components and actors), and educational Web services (for interoperability). In this ontology-based environment, actors interact with the LOs through educational servers, that manage (reuse, edit, delete, store) ontologies, and through tools which communicate with Web services to collect resources and links to other tools. Digital geological mapping involves a location-based, spatial organization of geological elements in a set of GIS thematic layers. Each layer in the stack assembles a set of polygonal (e.g., formation, member, intrusion), linear (e.g., fault, contact), and/or point (e.g., sample or measurement site) geological elements. These feature classes, represented in domain ontologies by classes, have their own sets of property (attribute, association relation) and topological (e.g., overlap, adjacency, containment), and network (cross-cuttings; connectivity) relationships. Since geological mapping involves describing and depicting different aspects of each feature class (e.g., contact, formation, structure), the same geographic region may be investigated by different communities, for example, for its stratigraphy, rock type, structure, soil type, and isotopic and paleontological age, using sets of ontologies. These data can become interconnected applying the Semantic Web technologies, on the Linked Open Data Cloud, based on their underlying common geographic coordinates. Sets of geological data published on the Cloud will include multiple RDF links to Cloud's geospatial nodes such as GeoNames and Linked GeoData. During mapping, a device such as smartphone, laptop, or iPad, with GPS and GIS capability and a DBpedia Mobile client, can use the current position to discover and query all the geological linked data, and add new data to the thematic layers and publish them to the Cloud.

vSPARQL: A View Definition Language for the Semantic Web

PubMed Central

Shaw, Marianne; Detwiler, Landon T.; Noy, Natalya; Brinkley, James; Suciu, Dan

2010-01-01

Translational medicine applications would like to leverage the biological and biomedical ontologies, vocabularies, and data sets available on the semantic web. We present a general solution for RDF information set reuse inspired by database views. Our view definition language, vSPARQL, allows applications to specify the exact content that they are interested in and how that content should be restructured or modified. Applications can access relevant content by querying against these view definitions. We evaluate the expressivity of our approach by defining views for practical use cases and comparing our view definition language to existing query languages. PMID:20800106

Accessing multimedia content from mobile applications using semantic web technologies

NASA Astrophysics Data System (ADS)

Kreutel, Jörn; Gerlach, Andrea; Klekamp, Stefanie; Schulz, Kristin

2014-02-01

We describe the ideas and results of an applied research project that aims at leveraging the expressive power of semantic web technologies as a server-side backend for mobile applications that provide access to location and multimedia data and allow for a rich user experience in mobile scenarios, ranging from city and museum guides to multimedia enhancements of any kind of narrative content, including e-book applications. In particular, we will outline a reusable software architecture for both server-side functionality and native mobile platforms that is aimed at significantly decreasing the effort required for developing particular applications of that kind.

Effective Web and Desktop Retrieval with Enhanced Semantic Spaces

NASA Astrophysics Data System (ADS)

Daoud, Amjad M.

We describe the design and implementation of the NETBOOK prototype system for collecting, structuring and efficiently creating semantic vectors for concepts, noun phrases, and documents from a corpus of free full text ebooks available on the World Wide Web. Automatic generation of concept maps from correlated index terms and extracted noun phrases are used to build a powerful conceptual index of individual pages. To ensure scalabilty of our system, dimension reduction is performed using Random Projection [13]. Furthermore, we present a complete evaluation of the relative effectiveness of the NETBOOK system versus the Google Desktop [8].

Empowering Personalized Medicine with Big Data and Semantic Web Technology: Promises, Challenges, and Use Cases.

PubMed

Panahiazar, Maryam; Taslimitehrani, Vahid; Jadhav, Ashutosh; Pathak, Jyotishman

2014-10-01

In healthcare, big data tools and technologies have the potential to create significant value by improving outcomes while lowering costs for each individual patient. Diagnostic images, genetic test results and biometric information are increasingly generated and stored in electronic health records presenting us with challenges in data that is by nature high volume, variety and velocity, thereby necessitating novel ways to store, manage and process big data. This presents an urgent need to develop new, scalable and expandable big data infrastructure and analytical methods that can enable healthcare providers access knowledge for the individual patient, yielding better decisions and outcomes. In this paper, we briefly discuss the nature of big data and the role of semantic web and data analysis for generating "smart data" which offer actionable information that supports better decision for personalized medicine. In our view, the biggest challenge is to create a system that makes big data robust and smart for healthcare providers and patients that can lead to more effective clinical decision-making, improved health outcomes, and ultimately, managing the healthcare costs. We highlight some of the challenges in using big data and propose the need for a semantic data-driven environment to address them. We illustrate our vision with practical use cases, and discuss a path for empowering personalized medicine using big data and semantic web technology.

Design for Connecting Spatial Data Infrastructures with Sensor Web (sensdi)

NASA Astrophysics Data System (ADS)

Bhattacharya, D.; M., M.

2016-06-01

Integrating Sensor Web With Spatial Data Infrastructures (SENSDI) aims to extend SDIs with sensor web enablement, converging geospatial and built infrastructure, and implement test cases with sensor data and SDI. It is about research to harness the sensed environment by utilizing domain specific sensor data to create a generalized sensor webframework. The challenges being semantic enablement for Spatial Data Infrastructures, and connecting the interfaces of SDI with interfaces of Sensor Web. The proposed research plan is to Identify sensor data sources, Setup an open source SDI, Match the APIs and functions between Sensor Web and SDI, and Case studies like hazard applications, urban applications etc. We take up co-operative development of SDI best practices to enable a new realm of a location enabled and semantically enriched World Wide Web - the "Geospatial Web" or "Geosemantic Web" by setting up one to one correspondence between WMS, WFS, WCS, Metadata and 'Sensor Observation Service' (SOS); 'Sensor Planning Service' (SPS); 'Sensor Alert Service' (SAS); a service that facilitates asynchronous message interchange between users and services, and between two OGC-SWE services, called the 'Web Notification Service' (WNS). Hence in conclusion, it is of importance to geospatial studies to integrate SDI with Sensor Web. The integration can be done through merging the common OGC interfaces of SDI and Sensor Web. Multi-usability studies to validate integration has to be undertaken as future research.

A Formal Theory for Modular ERDF Ontologies

NASA Astrophysics Data System (ADS)

Analyti, Anastasia; Antoniou, Grigoris; Damásio, Carlos Viegas

The success of the Semantic Web is impossible without any form of modularity, encapsulation, and access control. In an earlier paper, we extended RDF graphs with weak and strong negation, as well as derivation rules. The ERDF #n-stable model semantics of the extended RDF framework (ERDF) is defined, extending RDF(S) semantics. In this paper, we propose a framework for modular ERDF ontologies, called modular ERDF framework, which enables collaborative reasoning over a set of ERDF ontologies, while support for hidden knowledge is also provided. In particular, the modular ERDF stable model semantics of modular ERDF ontologies is defined, extending the ERDF #n-stable model semantics. Our proposed framework supports local semantics and different points of view, local closed-world and open-world assumptions, and scoped negation-as-failure. Several complexity results are provided.

Structure Discovery in Large Semantic Graphs Using Extant Ontological Scaling and Descriptive Statistics

DOE Office of Scientific and Technical Information (OSTI.GOV)

al-Saffar, Sinan; Joslyn, Cliff A.; Chappell, Alan R.

As semantic datasets grow to be very large and divergent, there is a need to identify and exploit their inherent semantic structure for discovery and optimization. Towards that end, we present here a novel methodology to identify the semantic structures inherent in an arbitrary semantic graph dataset. We first present the concept of an extant ontology as a statistical description of the semantic relations present amongst the typed entities modeled in the graph. This serves as a model of the underlying semantic structure to aid in discovery and visualization. We then describe a method of ontological scaling in which themore » ontology is employed as a hierarchical scaling filter to infer different resolution levels at which the graph structures are to be viewed or analyzed. We illustrate these methods on three large and publicly available semantic datasets containing more than one billion edges each. Keywords-Semantic Web; Visualization; Ontology; Multi-resolution Data Mining;« less

The Virtual Learning Commons (VLC): Enabling Co-Innovation Across Disciplines

NASA Astrophysics Data System (ADS)

Pennington, D. D.; Gandara, A.; Del Rio, N.

2014-12-01

A key challenge for scientists addressing grand-challenge problems is identifying, understanding, and integrating potentially relevant methods, models and tools that that are rapidly evolving in the informatics community. Such tools are essential for effectively integrating data and models in complex research projects, yet it is often difficult to know what tools are available and it is not easy to understand or evaluate how they might be used in a given research context. The goal of the National Science Foundation-funded Virtual Learning Commons (VLC) is to improve awareness and understanding of emerging methodologies and technologies, facilitate individual and group evaluation of these, and trace the impact of innovations within and across teams, disciplines, and communities. The VLC is a Web-based social bookmarking site designed specifically to support knowledge exchange in research communities. It is founded on well-developed models of technology adoption, diffusion of innovation, and experiential learning. The VLC makes use of Web 2.0 (Social Web) and Web 3.0 (Semantic Web) approaches. Semantic Web approaches enable discovery of potentially relevant methods, models, and tools, while Social Web approaches enable collaborative learning about their function. The VLC is under development and the first release is expected Fall 2014.

Connecting long-tail scientists with big data centers using SaaS

NASA Astrophysics Data System (ADS)

Percivall, G. S.; Bermudez, L. E.

2012-12-01

Big data centers and long tail scientists represent two extremes in the geoscience research community. Interoperability and inter-use based on software-as-a-service (SaaS) increases access to big data holdings by this underserved community of scientists. Large, institutional data centers have long been recognized as vital resources in the geoscience community. Permanent data archiving and dissemination centers provide "access to the data and (are) a critical source of people who have experience in the use of the data and can provide advice and counsel for new applications." [NRC] The "long-tail of science" is the geoscience researchers that work separate from institutional data centers [Heidorn]. Long-tail scientists need to be efficient consumers of data from large, institutional data centers. Discussions in NSF EarthCube capture the challenges: "Like the vast majority of NSF-funded researchers, Alice (a long-tail scientist) works with limited resources. In the absence of suitable expertise and infrastructure, the apparently simple task that she assigns to her graduate student becomes an information discovery and management nightmare. Downloading and transforming datasets takes weeks." [Foster, et.al.] The long-tail metaphor points to methods to bridge the gap, i.e., the Web. A decade ago, OGC began building a geospatial information space using open, web standards for geoprocessing [ORM]. Recently, [Foster, et.al.] accurately observed that "by adopting, adapting, and applying semantic web and SaaS technologies, we can make the use of geoscience data as easy and convenient as consumption of online media." SaaS places web services into Cloud Computing. SaaS for geospatial is emerging rapidly building on the first-generation geospatial web, e.g., OGC Web Coverage Service [WCS] and the Data Access Protocol [DAP]. Several recent examples show progress in applying SaaS to geosciences: - NASA's Earth Data Coherent Web has a goal to improve science user experience using Web Services (e.g. W*S, SOAP, RESTful) to reduce barriers to using EOSDIS data [ECW]. - NASA's LANCE provides direct access to vast amounts of satellite data using the OGC Web Map Tile Service (WMTS). - NOAA's Unified Access Framework for Gridded Data (UAF Grid) is a web service based capability for direct access to a variety of datasets using netCDF, OPeNDAP, THREDDS, WMS and WCS. [UAF] Tools to access SaaS's are many and varied: some proprietary, others open source; some run in browsers, others are stand-alone applications. What's required is interoperability using web interfaces offered by the data centers. NOAA's UAF service stack supports Matlab, ArcGIS, Ferret, GrADS, Google Earth, IDV, LAS. Any SaaS that offers OGC Web Services (WMS, WFS, WCS) can be accessed by scores of clients [OGC]. While there has been much progress in the recent year toward offering web services for the long-tail of scientists, more needs to be done. Web services offer data access but more than access is needed for inter-use of data, e.g. defining data schemas that allow for data fusion, addressing coordinate systems, spatial geometry, and semantics for observations. Connecting long-tail scientists with large, data centers using SaaS and, in the future, semantic web, will address this large and currently underserved user community.

Gazetteer Brokering through Semantic Mediation

NASA Astrophysics Data System (ADS)

Hobona, G.; Bermudez, L. E.; Brackin, R.

2013-12-01

A gazetteer is a geographical directory containing some information regarding places. It provides names, location and other attributes for places which may include points of interest (e.g. buildings, oilfields and boreholes), and other features. These features can be published via web services conforming to the Gazetteer Application Profile of the Web Feature Service (WFS) standard of the Open Geospatial Consortium (OGC). Against the backdrop of advances in geophysical surveys, there has been a significant increase in the amount of data referenced to locations. Gazetteers services have played a significant role in facilitating access to such data, including through provision of specialized queries such as text, spatial and fuzzy search. Recent developments in the OGC have led to advances in gazetteers such as support for multilingualism, diacritics, and querying via advanced spatial constraints (e.g. search by radial search and nearest neighbor). A challenge remaining however, is that gazetteers produced by different organizations have typically been modeled differently. Inconsistencies from gazetteers produced by different organizations may include naming the same feature in a different way, naming the attributes differently, locating the feature in a different location, and providing fewer or more attributes than the other services. The Gazetteer application profile of the WFS is a starting point to address such inconsistencies by providing a standardized interface based on rules specified in ISO 19112, the international standard for spatial referencing by geographic identifiers. The profile, however, does not provide rules to deal with semantic inconsistencies. The USGS and NGA commissioned research into the potential for a Single Point of Entry Global Gazetteer (SPEGG). The research was conducted by the Cross Community Interoperability thread of the OGC testbed, referenced OWS-9. The testbed prototyped approaches for brokering gazetteers through use of semantic web technologies, including ontologies and a semantic mediator. The semantically-enhanced SPEGG allowed a client to submit a single query (e.g. ';hills') and to retrieve data from two separate gazetteers with different vocabularies (e.g. where one refers to ';summits' another refers to ';hills'). Supporting the SPEGG was a SPARQL server that held the ontologies and processed queries on them. Earth Science surveys and forecast always have a place on Earth. Being able to share the information about a place and solve inconsistencies about that place from different sources will enable geoscientists to better do their research. In the advent of mobile geo computing and location based services (LBS), brokering gazetteers will provide geoscientists with access to gazetteer services rich with information and functionality beyond that offered by current generic gazetteers.

Semantic Web Compatible Names and Descriptions for Organisms

NASA Astrophysics Data System (ADS)

Wang, H.; Wilson, N.; McGuinness, D. L.

2012-12-01

Modern scientific names are critical for understanding the biological literature and provide a valuable way to understand evolutionary relationships. To validly publish a name, a description is required to separate the described group of organisms from those described by other names at the same level of the taxonomic hierarchy. The frequent revision of descriptions due to new evolutionary evidence has lead to situations where a single given scientific name may over time have multiple descriptions associated with it and a given published description may apply to multiple scientific names. Because of these many-to-many relationships between scientific names and descriptions, the usage of scientific names as a proxy for descriptions is inevitably ambiguous. Another issue lies in the fact that the precise application of scientific names often requires careful microscopic work, or increasingly, genetic sequencing, as scientific names are focused on the evolutionary relatedness between and within named groups such as species, genera, families, etc. This is problematic to many audiences, especially field biologists, who often do not have access to the instruments and tools required to make identifications on a microscopic or genetic basis. To better connect scientific names to descriptions and find a more convenient way to support computer assisted identification, we proposed the Semantic Vernacular System, a novel naming system that creates named, machine-interpretable descriptions for groups of organisms, and is compatible with the Semantic Web. Unlike the evolutionary relationship based scientific naming system, it emphasizes the observable features of organisms. By independently naming the descriptions composed of sets of observational features, as well as maintaining connections to scientific names, it preserves the observational data used to identify organisms. The system is designed to support a peer-review mechanism for creating new names, and uses a controlled vocabulary encoded in the Web Ontology Language to represent the observational features. A prototype of the system is currently under development in collaboration with the Mushroom Observer website. It allows users to propose new names and descriptions for fungi, provide feedback on those proposals, and ultimately have them formally approved. It relies on SPARQL queries and semantic reasoning for data management. This effort will offer the mycology community a knowledge base of fungal observational features and a tool for identifying fungal observations. It will also serve as an operational specification of how the Semantic Vernacular System can be used in practice in one scientific community (in this case mycology).

A Pilot Study on Modeling of Diagnostic Criteria Using OWL and SWRL.

PubMed

Hong, Na; Jiang, Guoqian; Pathak, Jyotishiman; Chute, Christopher G

2015-01-01

The objective of this study is to describe our efforts in a pilot study on modeling diagnostic criteria using a Semantic Web-based approach. We reused the basic framework of the ICD-11 content model and refined it into an operational model in the Web Ontology Language (OWL). The refinement is based on a bottom-up analysis method, in which we analyzed data elements (including value sets) in a collection (n=20) of randomly selected diagnostic criteria. We also performed a case study to formalize rule logic in the diagnostic criteria of metabolic syndrome using the Semantic Web Rule Language (SWRL). The results demonstrated that it is feasible to use OWL and SWRL to formalize the diagnostic criteria knowledge, and to execute the rules through reasoning.

Minimally inconsistent reasoning in Semantic Web.

PubMed

Zhang, Xiaowang

2017-01-01

Reasoning with inconsistencies is an important issue for Semantic Web as imperfect information is unavoidable in real applications. For this, different paraconsistent approaches, due to their capacity to draw as nontrivial conclusions by tolerating inconsistencies, have been proposed to reason with inconsistent description logic knowledge bases. However, existing paraconsistent approaches are often criticized for being too skeptical. To this end, this paper presents a non-monotonic paraconsistent version of description logic reasoning, called minimally inconsistent reasoning, where inconsistencies tolerated in the reasoning are minimized so that more reasonable conclusions can be inferred. Some desirable properties are studied, which shows that the new semantics inherits advantages of both non-monotonic reasoning and paraconsistent reasoning. A complete and sound tableau-based algorithm, called multi-valued tableaux, is developed to capture the minimally inconsistent reasoning. In fact, the tableaux algorithm is designed, as a framework for multi-valued DL, to allow for different underlying paraconsistent semantics, with the mere difference in the clash conditions. Finally, the complexity of minimally inconsistent description logic reasoning is shown on the same level as the (classical) description logic reasoning.

Minimally inconsistent reasoning in Semantic Web

PubMed Central

Zhang, Xiaowang

2017-01-01

Reasoning with inconsistencies is an important issue for Semantic Web as imperfect information is unavoidable in real applications. For this, different paraconsistent approaches, due to their capacity to draw as nontrivial conclusions by tolerating inconsistencies, have been proposed to reason with inconsistent description logic knowledge bases. However, existing paraconsistent approaches are often criticized for being too skeptical. To this end, this paper presents a non-monotonic paraconsistent version of description logic reasoning, called minimally inconsistent reasoning, where inconsistencies tolerated in the reasoning are minimized so that more reasonable conclusions can be inferred. Some desirable properties are studied, which shows that the new semantics inherits advantages of both non-monotonic reasoning and paraconsistent reasoning. A complete and sound tableau-based algorithm, called multi-valued tableaux, is developed to capture the minimally inconsistent reasoning. In fact, the tableaux algorithm is designed, as a framework for multi-valued DL, to allow for different underlying paraconsistent semantics, with the mere difference in the clash conditions. Finally, the complexity of minimally inconsistent description logic reasoning is shown on the same level as the (classical) description logic reasoning. PMID:28750030

GOssTo: a stand-alone application and a web tool for calculating semantic similarities on the Gene Ontology.

PubMed

Caniza, Horacio; Romero, Alfonso E; Heron, Samuel; Yang, Haixuan; Devoto, Alessandra; Frasca, Marco; Mesiti, Marco; Valentini, Giorgio; Paccanaro, Alberto

2014-08-01

We present GOssTo, the Gene Ontology semantic similarity Tool, a user-friendly software system for calculating semantic similarities between gene products according to the Gene Ontology. GOssTo is bundled with six semantic similarity measures, including both term- and graph-based measures, and has extension capabilities to allow the user to add new similarities. Importantly, for any measure, GOssTo can also calculate the Random Walk Contribution that has been shown to greatly improve the accuracy of similarity measures. GOssTo is very fast, easy to use, and it allows the calculation of similarities on a genomic scale in a few minutes on a regular desktop machine. alberto@cs.rhul.ac.uk GOssTo is available both as a stand-alone application running on GNU/Linux, Windows and MacOS from www.paccanarolab.org/gossto and as a web application from www.paccanarolab.org/gosstoweb. The stand-alone application features a simple and concise command line interface for easy integration into high-throughput data processing pipelines. © The Author 2014. Published by Oxford University Press.

Providing Knowledge Recommendations: An Approach for Informal Electronic Mentoring

ERIC Educational Resources Information Center

Colomo-Palacios, Ricardo; Casado-Lumbreras, Cristina; Soto-Acosta, Pedro; Misra, Sanjay

2014-01-01

The use of Web 2.0 technologies for knowledge management is invading the corporate sphere. The Web 2.0 is the most adopted knowledge transfer tool within knowledge intensive firms and is starting to be used for mentoring. This paper presents IM-TAG, a Web 2.0 tool, based on semantic technologies, for informal mentoring. The tool offers…

Network-Based Learning and Assessment Applications on the Semantic Web

ERIC Educational Resources Information Center

Gibson, David

2005-01-01

Today's Web applications are already "aware" of the network of computers and data on the Internet, in the sense that they perceive, remember, and represent knowledge external to themselves. However, Web applications are generally not able to respond to the meaning and context of the information in their memories. As a result, most applications are…

A bibliometric and visual analysis of global geo-ontology research

NASA Astrophysics Data System (ADS)

Li, Lin; Liu, Yu; Zhu, Haihong; Ying, Shen; Luo, Qinyao; Luo, Heng; Kuai, Xi; Xia, Hui; Shen, Hang

2017-02-01

In this paper, the results of a bibliometric and visual analysis of geo-ontology research articles collected from the Web of Science (WOS) database between 1999 and 2014 are presented. The numbers of national institutions and published papers are visualized and a global research heat map is drawn, illustrating an overview of global geo-ontology research. In addition, we present a chord diagram of countries and perform a visual cluster analysis of a knowledge co-citation network of references, disclosing potential academic communities and identifying key points, main research areas, and future research trends. The International Journal of Geographical Information Science, Progress in Human Geography, and Computers & Geosciences are the most active journals. The USA makes the largest contributions to geo-ontology research by virtue of its highest numbers of independent and collaborative papers, and its dominance was also confirmed in the country chord diagram. The majority of institutions are in the USA, Western Europe, and Eastern Asia. Wuhan University, University of Munster, and the Chinese Academy of Sciences are notable geo-ontology institutions. Keywords such as "Semantic Web," "GIS," and "space" have attracted a great deal of attention. "Semantic granularity in ontology-driven geographic information systems, "Ontologies in support of activities in geographical space" and "A translation approach to portable ontology specifications" have the highest cited centrality. Geographical space, computer-human interaction, and ontology cognition are the three main research areas of geo-ontology. The semantic mismatch between the producers and users of ontology data as well as error propagation in interdisciplinary and cross-linguistic data reuse needs to be solved. In addition, the development of geo-ontology modeling primitives based on OWL (Web Ontology Language）and finding methods to automatically rework data in Semantic Web are needed. Furthermore, the topological relations between geographical entities still require further study.

Comparison: Mediation Solutions of WSMOLX and WebML/WebRatio

NASA Astrophysics Data System (ADS)

Zaremba, Maciej; Zaharia, Raluca; Turati, Andrea; Brambilla, Marco; Vitvar, Tomas; Ceri, Stefano

In this chapter we compare the WSMO/WSML/WSMX andWebML/WebRatio approaches to the SWS-Challenge workshop mediation scenario in terms of the utilized underlying technologies and delivered solutions. In the mediation scenario one partner uses Roset-taNet to define its B2B protocol while the other one operates on a proprietary solution. Both teams shown how these partners could be semantically integrated.

BioPortal: An Open-Source Community-Based Ontology Repository

NASA Astrophysics Data System (ADS)

Noy, N.; NCBO Team

2011-12-01

Advances in computing power and new computational techniques have changed the way researchers approach science. In many fields, one of the most fruitful approaches has been to use semantically aware software to break down the barriers among disparate domains, systems, data sources, and technologies. Such software facilitates data aggregation, improves search, and ultimately allows the detection of new associations that were previously not detectable. Achieving these analyses requires software systems that take advantage of the semantics and that can intelligently negotiate domains and knowledge sources, identifying commonality across systems that use different and conflicting vocabularies, while understanding apparent differences that may be concealed by the use of superficially similar terms. An ontology, a semantically rich vocabulary for a domain of interest, is the cornerstone of software for bridging systems, domains, and resources. However, as ontologies become the foundation of all semantic technologies in e-science, we must develop an infrastructure for sharing ontologies, finding and evaluating them, integrating and mapping among them, and using ontologies in applications that help scientists process their data. BioPortal [1] is an open-source on-line community-based ontology repository that has been used as a critical component of semantic infrastructure in several domains, including biomedicine and bio-geochemical data. BioPortal, uses the social approaches in the Web 2.0 style to bring structure and order to the collection of biomedical ontologies. It enables users to provide and discuss a wide array of knowledge components, from submitting the ontologies themselves, to commenting on and discussing classes in the ontologies, to reviewing ontologies in the context of their own ontology-based projects, to creating mappings between overlapping ontologies and discussing and critiquing the mappings. Critically, it provides web-service access to all its content, enabling its integration in semantically enriched applications. [1] Noy, N.F., Shah, N.H., et al., BioPortal: ontologies and integrated data resources at the click of a mouse. Nucleic Acids Res, 2009. 37(Web Server issue): p. W170-3.

A technological infrastructure to sustain Internetworked Enterprises

NASA Astrophysics Data System (ADS)

La Mattina, Ernesto; Savarino, Vincenzo; Vicari, Claudia; Storelli, Davide; Bianchini, Devis

In the Web 3.0 scenario, where information and services are connected by means of their semantics, organizations can improve their competitive advantage by publishing their business and service descriptions. In this scenario, Semantic Peer to Peer (P2P) can play a key role in defining dynamic and highly reconfigurable infrastructures. Organizations can share knowledge and services, using this infrastructure to move towards value networks, an emerging organizational model characterized by fluid boundaries and complex relationships. This chapter collects and defines the technological requirements and architecture of a modular and multi-Layer Peer to Peer infrastructure for SOA-based applications. This technological infrastructure, based on the combination of Semantic Web and P2P technologies, is intended to sustain Internetworked Enterprise configurations, defining a distributed registry and enabling more expressive queries and efficient routing mechanisms. The following sections focus on the overall architecture, while describing the layers that form it.

A Process for the Representation of openEHR ADL Archetypes in OWL Ontologies.

PubMed

Porn, Alex Mateus; Peres, Leticia Mara; Didonet Del Fabro, Marcos

2015-01-01

ADL is a formal language to express archetypes, independent of standards or domain. However, its specification is not precise enough in relation to the specialization and semantic of archetypes, presenting difficulties in implementation and a few available tools. Archetypes may be implemented using other languages such as XML or OWL, increasing integration with Semantic Web tools. Exchanging and transforming data can be better implemented with semantics oriented models, for example using OWL which is a language to define and instantiate Web ontologies defined by W3C. OWL permits defining significant, detailed, precise and consistent distinctions among classes, properties and relations by the user, ensuring the consistency of knowledge than using ADL techniques. This paper presents a process of an openEHR ADL archetypes representation in OWL ontologies. This process consists of ADL archetypes conversion in OWL ontologies and validation of OWL resultant ontologies using the mutation test.

Sharing Epigraphic Information as Linked Data

NASA Astrophysics Data System (ADS)

Álvarez, Fernando-Luis; García-Barriocanal, Elena; Gómez-Pantoja, Joaquín-L.

The diffusion of epigraphic data has evolved in the last years from printed catalogues to indexed digital databases shared through the Web. Recently, the open EpiDoc specifications have resulted in an XML-based schema for the interchange of ancient texts that uses XSLT to render typographic representations. However, these schemas and representation systems are still not providing a way to encode computational semantics and semantic relations between pieces of epigraphic data. This paper sketches an approach to bring these semantics into an EpiDoc based schema using the Ontology Web Language (OWL) and following the principles and methods of information sharing known as "linked data". The paper describes the general principles of the OWL mapping of the EpiDoc schema and how epigraphic data can be shared in RDF format via dereferenceable URIs that can be used to build advanced search, visualization and analysis systems.

Dynamic User Interfaces for Service Oriented Architectures in Healthcare.

PubMed

Schweitzer, Marco; Hoerbst, Alexander

2016-01-01

Electronic Health Records (EHRs) play a crucial role in healthcare today. Considering a data-centric view, EHRs are very advanced as they provide and share healthcare data in a cross-institutional and patient-centered way adhering to high syntactic and semantic interoperability. However, the EHR functionalities available for the end users are rare and hence often limited to basic document query functions. Future EHR use necessitates the ability to let the users define their needed data according to a certain situation and how this data should be processed. Workflow and semantic modelling approaches as well as Web services provide means to fulfil such a goal. This thesis develops concepts for dynamic interfaces between EHR end users and a service oriented eHealth infrastructure, which allow the users to design their flexible EHR needs, modeled in a dynamic and formal way. These are used to discover, compose and execute the right Semantic Web services.

Semantic Metadata for Heterogeneous Spatial Planning Documents

NASA Astrophysics Data System (ADS)

Iwaniak, A.; Kaczmarek, I.; Łukowicz, J.; Strzelecki, M.; Coetzee, S.; Paluszyński, W.

2016-09-01

Spatial planning documents contain information about the principles and rights of land use in different zones of a local authority. They are the basis for administrative decision making in support of sustainable development. In Poland these documents are published on the Web according to a prescribed non-extendable XML schema, designed for optimum presentation to humans in HTML web pages. There is no document standard, and limited functionality exists for adding references to external resources. The text in these documents is discoverable and searchable by general-purpose web search engines, but the semantics of the content cannot be discovered or queried. The spatial information in these documents is geographically referenced but not machine-readable. Major manual efforts are required to integrate such heterogeneous spatial planning documents from various local authorities for analysis, scenario planning and decision support. This article presents results of an implementation using machine-readable semantic metadata to identify relationships among regulations in the text, spatial objects in the drawings and links to external resources. A spatial planning ontology was used to annotate different sections of spatial planning documents with semantic metadata in the Resource Description Framework in Attributes (RDFa). The semantic interpretation of the content, links between document elements and links to external resources were embedded in XHTML pages. An example and use case from the spatial planning domain in Poland is presented to evaluate its efficiency and applicability. The solution enables the automated integration of spatial planning documents from multiple local authorities to assist decision makers with understanding and interpreting spatial planning information. The approach is equally applicable to legal documents from other countries and domains, such as cultural heritage and environmental management.

70 FR 69562 - Office of Environmental Information; Request for Comment and Request for Information on System...

Federal Register 2010, 2011, 2012, 2013, 2014

2005-11-16

... Reference System (TRS) [see http://www.epa.gov/trs ] in order to better support future semantic Web needs... creation of glossaries for Web pages and documents, a common vocabulary for search engines, and in the...

Web Services Integration on the Fly

DTIC Science & Technology

2008-12-01

NETBEANS 6.1 AND VERSION CONTROL............................................28 1. NetBeans Integrated Development Environment (IDE) ................28 2...Forward and Reverse Engineering...................................................28 3. Implementation using NetBeans ...29 4. Subversion (SVN) for Version Control in NetBeans ......................29 O. PROTÉGÉ AUTHORING TOOL FOR SEMANTIC WEB

On the Semantics of SPARQL

NASA Astrophysics Data System (ADS)

Arenas, Marcelo; Gutierrez, Claudio; Pérez, Jorge

The Resource Description Framework (RDF) is the standard data model for representing information about World Wide Web resources. In January 2008, it was released the recommendation of the W3C for querying RDF data, a query language called SPARQL. In this chapter, we give a detailed description of the semantics of this language. We start by focusing on the definition of a formal semantics for the core part of SPARQL, and then move to the definition for the entire language, including all the features in the specification of SPARQL by the W3C such as blank nodes in graph patterns and bag semantics for solutions.

SOMWeb: a semantic web-based system for supporting collaboration of distributed medical communities of practice.

PubMed

Falkman, Göran; Gustafsson, Marie; Jontell, Mats; Torgersson, Olof

2008-08-26

Information technology (IT) support for remote collaboration of geographically distributed communities of practice (CoP) in health care must deal with a number of sociotechnical aspects of communication within the community. In the mid-1990s, participants of the Swedish Oral Medicine Network (SOMNet) began discussing patient cases in telephone conferences. The cases were distributed prior to the conferences using PowerPoint and email. For the technical support of online CoP, Semantic Web technologies can potentially fulfill needs of knowledge reuse, data exchange, and reasoning based on ontologies. However, more research is needed on the use of Semantic Web technologies in practice. The objectives of this research were to (1) study the communication of distributed health care professionals in oral medicine; (2) apply Semantic Web technologies to describe community data and oral medicine knowledge; (3) develop an online CoP, Swedish Oral Medicine Web (SOMWeb), centered on user-contributed case descriptions and meetings; and (4) evaluate SOMWeb and study how work practices change with IT support. Based on Java, and using the Web Ontology Language and Resource Description Framework for handling community data and oral medicine knowledge, SOMWeb was developed using a user-centered and iterative approach. For studying the work practices and evaluating the system, a mixed-method approach of interviews, observations, and a questionnaire was used. By May 2008, there were 90 registered users of SOMWeb, 93 cases had been added, and 18 meetings had utilized the system. The introduction of SOMWeb has improved the structure of meetings and their discussions, and a tenfold increase in the number of participants has been observed. Users submit cases to seek advice on diagnosis or treatment, to show an unusual case, or to create discussion. Identified barriers to submitting cases are lack of time, concern about whether the case is interesting enough, and showing gaps in one's own knowledge. Three levels of member participation are discernable: a core group that contributes most cases and most meeting feedback; an active group that participates often but only sometimes contribute cases and feedback; and a large peripheral group that seldom or never contribute cases or feedback. SOMWeb is beneficial for individual clinicians as well as for the SOMNet community. The system provides an opportunity for its members to share both high quality clinical practice knowledge and external evidence related to complex oral medicine cases. The foundation in Semantic Web technologies enables formalization and structuring of case data that can be used for further reasoning and research. Main success factors are the long history of collaboration between different disciplines, the user-centered development approach, the existence of a "champion" within the field, and nontechnical community aspects already being in place.

SOMWeb: A Semantic Web-Based System for Supporting Collaboration of Distributed Medical Communities of Practice

PubMed Central

Gustafsson, Marie; Jontell, Mats; Torgersson, Olof

2008-01-01

Background Information technology (IT) support for remote collaboration of geographically distributed communities of practice (CoP) in health care must deal with a number of sociotechnical aspects of communication within the community. In the mid-1990s, participants of the Swedish Oral Medicine Network (SOMNet) began discussing patient cases in telephone conferences. The cases were distributed prior to the conferences using PowerPoint and email. For the technical support of online CoP, Semantic Web technologies can potentially fulfill needs of knowledge reuse, data exchange, and reasoning based on ontologies. However, more research is needed on the use of Semantic Web technologies in practice. Objectives The objectives of this research were to (1) study the communication of distributed health care professionals in oral medicine; (2) apply Semantic Web technologies to describe community data and oral medicine knowledge; (3) develop an online CoP, Swedish Oral Medicine Web (SOMWeb), centered on user-contributed case descriptions and meetings; and (4) evaluate SOMWeb and study how work practices change with IT support. Methods Based on Java, and using the Web Ontology Language and Resource Description Framework for handling community data and oral medicine knowledge, SOMWeb was developed using a user-centered and iterative approach. For studying the work practices and evaluating the system, a mixed-method approach of interviews, observations, and a questionnaire was used. Results By May 2008, there were 90 registered users of SOMWeb, 93 cases had been added, and 18 meetings had utilized the system. The introduction of SOMWeb has improved the structure of meetings and their discussions, and a tenfold increase in the number of participants has been observed. Users submit cases to seek advice on diagnosis or treatment, to show an unusual case, or to create discussion. Identified barriers to submitting cases are lack of time, concern about whether the case is interesting enough, and showing gaps in one’s own knowledge. Three levels of member participation are discernable: a core group that contributes most cases and most meeting feedback; an active group that participates often but only sometimes contribute cases and feedback; and a large peripheral group that seldom or never contribute cases or feedback. Conclusions SOMWeb is beneficial for individual clinicians as well as for the SOMNet community. The system provides an opportunity for its members to share both high quality clinical practice knowledge and external evidence related to complex oral medicine cases. The foundation in Semantic Web technologies enables formalization and structuring of case data that can be used for further reasoning and research. Main success factors are the long history of collaboration between different disciplines, the user-centered development approach, the existence of a “champion” within the field, and nontechnical community aspects already being in place. PMID:18725355

vSPARQL: a view definition language for the semantic web.

PubMed

Shaw, Marianne; Detwiler, Landon T; Noy, Natalya; Brinkley, James; Suciu, Dan

2011-02-01

Translational medicine applications would like to leverage the biological and biomedical ontologies, vocabularies, and data sets available on the semantic web. We present a general solution for RDF information set reuse inspired by database views. Our view definition language, vSPARQL, allows applications to specify the exact content that they are interested in and how that content should be restructured or modified. Applications can access relevant content by querying against these view definitions. We evaluate the expressivity of our approach by defining views for practical use cases and comparing our view definition language to existing query languages. Copyright © 2010 Elsevier Inc. All rights reserved.

Using GBrowse 2.0 to visualize and share next-generation sequence data

PubMed Central

2013-01-01

GBrowse is a mature web-based genome browser that is suitable for deployment on both public and private web sites. It supports most of genome browser features, including qualitative and quantitative (wiggle) tracks, track uploading, track sharing, interactive track configuration, semantic zooming and limited smooth track panning. As of version 2.0, GBrowse supports next-generation sequencing (NGS) data by providing for the direct display of SAM and BAM sequence alignment files. SAM/BAM tracks provide semantic zooming and support both local and remote data sources. This article provides step-by-step instructions for configuring GBrowse to display NGS data. PMID:23376193

Designing a patient monitoring system for bipolar disorder using Semantic Web technologies.

PubMed

Thermolia, Chryssa; Bei, Ekaterini S; Petrakis, Euripides G M; Kritsotakis, Vangelis; Tsiknakis, Manolis; Sakkalis, Vangelis

2015-01-01

The new movement to personalize treatment plans and improve prediction capabilities is greatly facilitated by intelligent remote patient monitoring and risk prevention. This paper focuses on patients suffering from bipolar disorder, a mental illness characterized by severe mood swings. We exploit the advantages of Semantic Web and Electronic Health Record Technologies to develop a patient monitoring platform to support clinicians. Relying on intelligently filtering of clinical evidence-based information and individual-specific knowledge, we aim to provide recommendations for treatment and monitoring at appropriate time or concluding into alerts for serious shifts in mood and patients' non response to treatment.

An Approach to Semantic Interoperability for Improved Capability Exchanges in Federations of Systems

ERIC Educational Resources Information Center

Moschoglou, Georgios

2013-01-01

This study seeks an affirmative answer to the question whether a knowledge-based approach to system of systems interoperation using semantic web standards and technologies can provide the centralized control of the capability for exchanging data and services lacking in a federation of systems. Given the need to collect and share real-time…

Improving Concept-Based Web Image Retrieval by Mixing Semantically Similar Greek Queries

ERIC Educational Resources Information Center

Lazarinis, Fotis

2008-01-01

Purpose: Image searching is a common activity for web users. Search engines offer image retrieval services based on textual queries. Previous studies have shown that web searching is more demanding when the search is not in English and does not use a Latin-based language. The aim of this paper is to explore the behaviour of the major search…

The BCube Crawler: Web Scale Data and Service Discovery for EarthCube.

NASA Astrophysics Data System (ADS)

Lopez, L. A.; Khalsa, S. J. S.; Duerr, R.; Tayachow, A.; Mingo, E.

2014-12-01

Web-crawling, a core component of the NSF-funded BCube project, is researching and applying the use of big data technologies to find and characterize different types of web services, catalog interfaces, and data feeds such as the ESIP OpenSearch, OGC W*S, THREDDS, and OAI-PMH that describe or provide access to scientific datasets. Given the scale of the Internet, which challenges even large search providers such as Google, the BCube plan for discovering these web accessible services is to subdivide the problem into three smaller, more tractable issues. The first, to be able to discover likely sites where relevant data and data services might be found, the second, to be able to deeply crawl the sites discovered to find any data and services which might be present. Lastly, to leverage the use of semantic technologies to characterize the services and data found, and to filter out everything but those relevant to the geosciences. To address the first two challenges BCube uses an adapted version of Apache Nutch (which originated Hadoop), a web scale crawler, and Amazon's ElasticMapReduce service for flexibility and cost effectiveness. For characterization of the services found, BCube is examining existing web service ontologies for their applicability to our needs and will re-use and/or extend these in order to query for services with specific well-defined characteristics in scientific datasets such as the use of geospatial namespaces. The original proposal for the crawler won a grant from Amazon's academic program, which allowed us to become operational; we successfully tested the Bcube Crawler at web scale obtaining a significant corpus, sizeable enough to enable work on characterization of the services and data found. There is still plenty of work to be done, doing "smart crawls" by managing the frontier, developing and enhancing our scoring algorithms and fully implementing the semantic characterization technologies. We describe the current status of the project, our successes and issues encountered. The final goal of the BCube crawler project is to provide relevant data services to other projects on the EarthCube stack and third party partners so they can be brokered and used by a wider scientific community.

An Ontology-Based Approach to Incorporate User-Generated Geo-Content Into Sdi

NASA Astrophysics Data System (ADS)

Deng, D.-P.; Lemmens, R.

2011-08-01

The Web is changing the way people share and communicate information because of emergence of various Web technologies, which enable people to contribute information on the Web. User-Generated Geo-Content (UGGC) is a potential resource of geographic information. Due to the different production methods, UGGC often cannot fit in geographic information model. There is a semantic gap between UGGC and formal geographic information. To integrate UGGC into geographic information, this study conducts an ontology-based process to bridge this semantic gap. This ontology-based process includes five steps: Collection, Extraction, Formalization, Mapping, and Deployment. In addition, this study implements this process on Twitter messages, which is relevant to Japan Earthquake disaster. By using this process, we extract disaster relief information from Twitter messages, and develop a knowledge base for GeoSPARQL queries in disaster relief information.

Fish Ontology framework for taxonomy-based fish recognition

PubMed Central

Ali, Najib M.; Khan, Haris A.; Then, Amy Y-Hui; Ving Ching, Chong; Gaur, Manas

2017-01-01

Life science ontologies play an important role in Semantic Web. Given the diversity in fish species and the associated wealth of information, it is imperative to develop an ontology capable of linking and integrating this information in an automated fashion. As such, we introduce the Fish Ontology (FO), an automated classification architecture of existing fish taxa which provides taxonomic information on unknown fish based on metadata restrictions. It is designed to support knowledge discovery, provide semantic annotation of fish and fisheries resources, data integration, and information retrieval. Automated classification for unknown specimens is a unique feature that currently does not appear to exist in other known ontologies. Examples of automated classification for major groups of fish are demonstrated, showing the inferred information by introducing several restrictions at the species or specimen level. The current version of FO has 1,830 classes, includes widely used fisheries terminology, and models major aspects of fish taxonomy, grouping, and character. With more than 30,000 known fish species globally, the FO will be an indispensable tool for fish scientists and other interested users. PMID:28929028

Moving Controlled Vocabularies into the Semantic Web

NASA Astrophysics Data System (ADS)

Thomas, R.; Lowry, R. K.; Kokkinaki, A.

2015-12-01

One of the issues with legacy oceanographic data formats is that the only tool available for describing what a measurement is and how it was made is a single metadata tag known as the parameter code. The British Oceanographic Data Centre (BODC) has been supporting the international oceanographic community gain maximum benefit from this through a controlled vocabulary known as the BODC Parameter Usage Vocabulary (PUV). Over time this has grown to over 34,000 entries some of which have preferred labels with over 400 bytes of descriptive information detailing what was measured and how. A decade ago the BODC pioneered making this information available in a more useful form with the implementation of a prototype vocabulary server (NVS) that referenced each 'parameter code' as a URL. This developed into the current server (NVS V2) in which the parameter URL resolves into an RDF document based on the SKOS data model which includes a list of resource URLs mapped to the 'parameter'. For example the parameter code for a contaminant in biota, such as 'cadmium in Mytilus edulis', carries RDF triples leading to the entry for Mytilus edulis in the WoRMS and for cadmium in the ChEBI ontologies. By providing links into these external ontologies the information captured in a 1980s parameter code now conforms to the Linked Data paradigm of the Semantic Web, vastly increasing the descriptive information accessible to a user. This presentation will describe the next steps along the road to the Semantic Web with the development of a SPARQL end point1 to expose the PUV plus the 190 other controlled vocabularies held in NVS. Whilst this is ideal for those fluent in SPARQL, most users require something a little more user-friendly and so the NVS browser2 was developed over the end point to allow less technical users to query the vocabularies and navigate the NVS ontology. This tool integrates into an editor that allows vocabulary content to be manipulated by authorised users outside BODC. Having placed Linked Data tooling over a single SPARQL end point the obvious future development for this system is to support semantic interoperability outside NVS by the incorporation of federated SPARQL end points in the USA and Australia during the ODIP II project. 1https://vocab.nerc.ac.uk/sparql 2 https://www.bodc.ac.uk/data/codes_and_formats/vocabulary_search/

XML Based Markup Languages for Specific Domains

NASA Astrophysics Data System (ADS)

Varde, Aparna; Rundensteiner, Elke; Fahrenholz, Sally

A challenging area in web based support systems is the study of human activities in connection with the web, especially with reference to certain domains. This includes capturing human reasoning in information retrieval, facilitating the exchange of domain-specific knowledge through a common platform and developing tools for the analysis of data on the web from a domain expert's angle. Among the techniques and standards related to such work, we have XML, the eXtensible Markup Language. This serves as a medium of communication for storing and publishing textual, numeric and other forms of data seamlessly. XML tag sets are such that they preserve semantics and simplify the understanding of stored information by users. Often domain-specific markup languages are designed using XML, with a user-centric perspective. Standardization bodies and research communities may extend these to include additional semantics of areas within and related to the domain. This chapter outlines the issues to be considered in developing domain-specific markup languages: the motivation for development, the semantic considerations, the syntactic constraints and other relevant aspects, especially taking into account human factors. Illustrating examples are provided from domains such as Medicine, Finance and Materials Science. Particular emphasis in these examples is on the Materials Markup Language MatML and the semantics of one of its areas, namely, the Heat Treating of Materials. The focus of this chapter, however, is not the design of one particular language but rather the generic issues concerning the development of domain-specific markup languages.

Education in Biomedical and Health Informatics in the Web 3.0 Era: Standards for data, curricula, and activities. Contribution of the IMIA Working Group on Health and Medical Informatics Education.

PubMed

Otero, P; Hersh, W

2011-01-01

Web 3.0 is transforming the World Wide Web by allowing knowledge and reasoning to be gleaned from its content. Describe a new scenario in education and training known as "Education 3.0" that can help in the promotion of learning in health informatics in a collaborative way. Review of the current standards available for curricula and learning activities in in Biomedical and Health Informatics (BMHI) for a Web 3.0 scenario. A new scenario known as "Education 3.0" can provide open educational resources created and reused throughout different institutions and improved by means of an international collaborative knowledge powered by the use of E-learning. Currently there are standards that could be used in identifying and deliver content in education in BMHI in the semantic web era such as Resource Description Format (RDF), Web Ontology Language (OWL) and Sharable Content Object Reference Model (SCORM). In addition, there are other standards to support healthcare education and training. There are few experiences in the use of standards in e-learning in BMHI published in the literature. Web 3.0 can propose new approaches to building the BMHI workforce so there is a need to build tools as knowledge infrastructure to leverage it. The usefulness of standards in the content and competencies of training programs in BMHI needs more experience and research so as to promote the interoperability and sharing of resources in this growing discipline.

A Digital Knowledge Preservation Platform for Environmental Sciences

NASA Astrophysics Data System (ADS)

Aguilar Gómez, Fernando; de Lucas, Jesús Marco; Pertinez, Esther; Palacio, Aida; Perez, David

2017-04-01

The Digital Knowledge Preservation Platform is the evolution of a pilot project for Open Data supporting the full research data life cycle. It is currently being evolved at IFCA (Instituto de Física de Cantabria) as a combination of different open tools that have been extended: DMPTool (https://dmptool.org/) with pilot semantics features (RDF export, parameters definition), INVENIO (http://invenio-software.org/ ) customized version to integrate the entire research data life cycle and Jupyter (http://jupyter.org/) as processing tool and reproducibility environment. This complete platform aims to provide an integrated environment for research data management following the FAIR+R principles: -Findable: The Web portal based on Invenio provides a search engine and all elements including metadata to make them easily findable. -Accessible: Both data and software are available online with internal PIDs and DOIs (provided by Datacite). -Interoperable: Datasets can be combined to perform new analysis. The OAI-PMH standard is also integrated. -Re-usable: different licenses types and embargo periods can be defined. -+Reproducible: directly integrated with cloud computing resources. The deployment of the entire system over a Cloud framework helps to build a dynamic and scalable solution, not only for managing open datasets but also as a useful tool for the final user, who is able to directly process and analyse the open data. In parallel, the direct use of semantics and metadata is being explored and integrated in the framework. Ontologies, being a knowledge representation, can contribute to define the elements and relationships of the research data life cycle, including DMP, datasets, software, etc. The first advantage of developing an ontology of a knowledge domain is that they provide a common vocabulary hierarchy (i.e. a conceptual schema) that can be used and standardized by all the agents interested in the domain (either humans or machines). This way of using ontologies is one of the basis of the Semantic Web, where ontologies are set to play a key role in establishing a common terminology between agents. To develop the ontology we are using a graphical tool called Protégé. Protégé is a graphical ontology-development tool which supports a rich knowledge model and it is open-source and freely available. However in order to process and manage the ontology from the web framework, we are using Semantic MediaWiki, which is able to process queries. Semantic MediaWiki is an extension of MediaWiki where we can do semantic search and export data in RDF and CSV format. This system is used as a testbed for the potential use of semantics in a more general environment. This Digital Knowledge Preservation Platform is very closed related to INDIGO-DataCloud project (https://www.indigo-datacloud.eu) since the same data life cycle approach is taking into account (Planning, Collect, Curate, Analyze, Publish, Preserve). INDIGO-DataCloud solutions will be able to support all the different elements in the system, as we showed in the last Research Data Alliance Plenary. This presentation will show the different elements on the system and how they work, as well as the roadmap of their continuous integration.

Building a transnational biosurveillance network using semantic web technologies: requirements, design, and preliminary evaluation.

PubMed

Teodoro, Douglas; Pasche, Emilie; Gobeill, Julien; Emonet, Stéphane; Ruch, Patrick; Lovis, Christian

2012-05-29

Antimicrobial resistance has reached globally alarming levels and is becoming a major public health threat. Lack of efficacious antimicrobial resistance surveillance systems was identified as one of the causes of increasing resistance, due to the lag time between new resistances and alerts to care providers. Several initiatives to track drug resistance evolution have been developed. However, no effective real-time and source-independent antimicrobial resistance monitoring system is available publicly. To design and implement an architecture that can provide real-time and source-independent antimicrobial resistance monitoring to support transnational resistance surveillance. In particular, we investigated the use of a Semantic Web-based model to foster integration and interoperability of interinstitutional and cross-border microbiology laboratory databases. Following the agile software development methodology, we derived the main requirements needed for effective antimicrobial resistance monitoring, from which we proposed a decentralized monitoring architecture based on the Semantic Web stack. The architecture uses an ontology-driven approach to promote the integration of a network of sentinel hospitals or laboratories. Local databases are wrapped into semantic data repositories that automatically expose local computing-formalized laboratory information in the Web. A central source mediator, based on local reasoning, coordinates the access to the semantic end points. On the user side, a user-friendly Web interface provides access and graphical visualization to the integrated views. We designed and implemented the online Antimicrobial Resistance Trend Monitoring System (ARTEMIS) in a pilot network of seven European health care institutions sharing 70+ million triples of information about drug resistance and consumption. Evaluation of the computing performance of the mediator demonstrated that, on average, query response time was a few seconds (mean 4.3, SD 0.1 × 10(2) seconds). Clinical pertinence assessment showed that resistance trends automatically calculated by ARTEMIS had a strong positive correlation with the European Antimicrobial Resistance Surveillance Network (EARS-Net) (ρ = .86, P < .001) and the Sentinel Surveillance of Antibiotic Resistance in Switzerland (SEARCH) (ρ = .84, P < .001) systems. Furthermore, mean resistance rates extracted by ARTEMIS were not significantly different from those of either EARS-Net (∆ = ±0.130; 95% confidence interval -0 to 0.030; P < .001) or SEARCH (∆ = ±0.042; 95% confidence interval -0.004 to 0.028; P = .004). We introduce a distributed monitoring architecture that can be used to build transnational antimicrobial resistance surveillance networks. Results indicated that the Semantic Web-based approach provided an efficient and reliable solution for development of eHealth architectures that enable online antimicrobial resistance monitoring from heterogeneous data sources. In future, we expect that more health care institutions can join the ARTEMIS network so that it can provide a large European and wider biosurveillance network that can be used to detect emerging bacterial resistance in a multinational context and support public health actions.

Building a Transnational Biosurveillance Network Using Semantic Web Technologies: Requirements, Design, and Preliminary Evaluation

PubMed Central

Pasche, Emilie; Gobeill, Julien; Emonet, Stéphane; Ruch, Patrick; Lovis, Christian

2012-01-01

Background Antimicrobial resistance has reached globally alarming levels and is becoming a major public health threat. Lack of efficacious antimicrobial resistance surveillance systems was identified as one of the causes of increasing resistance, due to the lag time between new resistances and alerts to care providers. Several initiatives to track drug resistance evolution have been developed. However, no effective real-time and source-independent antimicrobial resistance monitoring system is available publicly. Objective To design and implement an architecture that can provide real-time and source-independent antimicrobial resistance monitoring to support transnational resistance surveillance. In particular, we investigated the use of a Semantic Web-based model to foster integration and interoperability of interinstitutional and cross-border microbiology laboratory databases. Methods Following the agile software development methodology, we derived the main requirements needed for effective antimicrobial resistance monitoring, from which we proposed a decentralized monitoring architecture based on the Semantic Web stack. The architecture uses an ontology-driven approach to promote the integration of a network of sentinel hospitals or laboratories. Local databases are wrapped into semantic data repositories that automatically expose local computing-formalized laboratory information in the Web. A central source mediator, based on local reasoning, coordinates the access to the semantic end points. On the user side, a user-friendly Web interface provides access and graphical visualization to the integrated views. Results We designed and implemented the online Antimicrobial Resistance Trend Monitoring System (ARTEMIS) in a pilot network of seven European health care institutions sharing 70+ million triples of information about drug resistance and consumption. Evaluation of the computing performance of the mediator demonstrated that, on average, query response time was a few seconds (mean 4.3, SD 0.1×102 seconds). Clinical pertinence assessment showed that resistance trends automatically calculated by ARTEMIS had a strong positive correlation with the European Antimicrobial Resistance Surveillance Network (EARS-Net) (ρ = .86, P < .001) and the Sentinel Surveillance of Antibiotic Resistance in Switzerland (SEARCH) (ρ = .84, P < .001) systems. Furthermore, mean resistance rates extracted by ARTEMIS were not significantly different from those of either EARS-Net (∆ = ±0.130; 95% confidence interval –0 to 0.030; P < .001) or SEARCH (∆ = ±0.042; 95% confidence interval –0.004 to 0.028; P = .004). Conclusions We introduce a distributed monitoring architecture that can be used to build transnational antimicrobial resistance surveillance networks. Results indicated that the Semantic Web-based approach provided an efficient and reliable solution for development of eHealth architectures that enable online antimicrobial resistance monitoring from heterogeneous data sources. In future, we expect that more health care institutions can join the ARTEMIS network so that it can provide a large European and wider biosurveillance network that can be used to detect emerging bacterial resistance in a multinational context and support public health actions. PMID:22642960

Harnessing Big Data for Systems Pharmacology

PubMed Central

Xie, Lei; Draizen, Eli J.; Bourne, Philip E.

2017-01-01

Systems pharmacology aims to holistically understand mechanisms of drug actions to support drug discovery and clinical practice. Systems pharmacology modeling (SPM) is data driven. It integrates an exponentially growing amount of data at multiple scales (genetic, molecular, cellular, organismal, and environmental). The goal of SPM is to develop mechanistic or predictive multiscale models that are interpretable and actionable. The current explosions in genomics and other omics data, as well as the tremendous advances in big data technologies, have already enabled biologists to generate novel hypotheses and gain new knowledge through computational models of genome-wide, heterogeneous, and dynamic data sets. More work is needed to interpret and predict a drug response phenotype, which is dependent on many known and unknown factors. To gain a comprehensive understanding of drug actions, SPM requires close collaborations between domain experts from diverse fields and integration of heterogeneous models from biophysics, mathematics, statistics, machine learning, and semantic webs. This creates challenges in model management, model integration, model translation, and knowledge integration. In this review, we discuss several emergent issues in SPM and potential solutions using big data technology and analytics. The concurrent development of high-throughput techniques, cloud computing, data science, and the semantic web will likely allow SPM to be findable, accessible, interoperable, reusable, reliable, interpretable, and actionable. PMID:27814027

Harnessing Big Data for Systems Pharmacology.

PubMed

Xie, Lei; Draizen, Eli J; Bourne, Philip E

2017-01-06

Systems pharmacology aims to holistically understand mechanisms of drug actions to support drug discovery and clinical practice. Systems pharmacology modeling (SPM) is data driven. It integrates an exponentially growing amount of data at multiple scales (genetic, molecular, cellular, organismal, and environmental). The goal of SPM is to develop mechanistic or predictive multiscale models that are interpretable and actionable. The current explosions in genomics and other omics data, as well as the tremendous advances in big data technologies, have already enabled biologists to generate novel hypotheses and gain new knowledge through computational models of genome-wide, heterogeneous, and dynamic data sets. More work is needed to interpret and predict a drug response phenotype, which is dependent on many known and unknown factors. To gain a comprehensive understanding of drug actions, SPM requires close collaborations between domain experts from diverse fields and integration of heterogeneous models from biophysics, mathematics, statistics, machine learning, and semantic webs. This creates challenges in model management, model integration, model translation, and knowledge integration. In this review, we discuss several emergent issues in SPM and potential solutions using big data technology and analytics. The concurrent development of high-throughput techniques, cloud computing, data science, and the semantic web will likely allow SPM to be findable, accessible, interoperable, reusable, reliable, interpretable, and actionable.

Structuring and extracting knowledge for the support of hypothesis generation in molecular biology

PubMed Central

Roos, Marco; Marshall, M Scott; Gibson, Andrew P; Schuemie, Martijn; Meij, Edgar; Katrenko, Sophia; van Hage, Willem Robert; Krommydas, Konstantinos; Adriaans, Pieter W

2009-01-01

Background Hypothesis generation in molecular and cellular biology is an empirical process in which knowledge derived from prior experiments is distilled into a comprehensible model. The requirement of automated support is exemplified by the difficulty of considering all relevant facts that are contained in the millions of documents available from PubMed. Semantic Web provides tools for sharing prior knowledge, while information retrieval and information extraction techniques enable its extraction from literature. Their combination makes prior knowledge available for computational analysis and inference. While some tools provide complete solutions that limit the control over the modeling and extraction processes, we seek a methodology that supports control by the experimenter over these critical processes. Results We describe progress towards automated support for the generation of biomolecular hypotheses. Semantic Web technologies are used to structure and store knowledge, while a workflow extracts knowledge from text. We designed minimal proto-ontologies in OWL for capturing different aspects of a text mining experiment: the biological hypothesis, text and documents, text mining, and workflow provenance. The models fit a methodology that allows focus on the requirements of a single experiment while supporting reuse and posterior analysis of extracted knowledge from multiple experiments. Our workflow is composed of services from the 'Adaptive Information Disclosure Application' (AIDA) toolkit as well as a few others. The output is a semantic model with putative biological relations, with each relation linked to the corresponding evidence. Conclusion We demonstrated a 'do-it-yourself' approach for structuring and extracting knowledge in the context of experimental research on biomolecular mechanisms. The methodology can be used to bootstrap the construction of semantically rich biological models using the results of knowledge extraction processes. Models specific to particular experiments can be constructed that, in turn, link with other semantic models, creating a web of knowledge that spans experiments. Mapping mechanisms can link to other knowledge resources such as OBO ontologies or SKOS vocabularies. AIDA Web Services can be used to design personalized knowledge extraction procedures. In our example experiment, we found three proteins (NF-Kappa B, p21, and Bax) potentially playing a role in the interplay between nutrients and epigenetic gene regulation. PMID:19796406

Generating Researcher Networks with Identified Persons on a Semantic Service Platform

NASA Astrophysics Data System (ADS)

Jung, Hanmin; Lee, Mikyoung; Kim, Pyung; Lee, Seungwoo

This paper describes a Semantic Web-based method to acquire researcher networks by means of identification scheme, ontology, and reasoning. Three steps are required to realize it; resolving co-references, finding experts, and generating researcher networks. We adopt OntoFrame as an underlying semantic service platform and apply reasoning to make direct relations between far-off classes in ontology schema. 453,124 Elsevier journal articles with metadata and full-text documents in information technology and biomedical domains have been loaded and served on the platform as a test set.

Neuroimaging, Genetics, and Clinical Data Sharing in Python Using the CubicWeb Framework

PubMed Central

Grigis, Antoine; Goyard, David; Cherbonnier, Robin; Gareau, Thomas; Papadopoulos Orfanos, Dimitri; Chauvat, Nicolas; Di Mascio, Adrien; Schumann, Gunter; Spooren, Will; Murphy, Declan; Frouin, Vincent

2017-01-01

In neurosciences or psychiatry, the emergence of large multi-center population imaging studies raises numerous technological challenges. From distributed data collection, across different institutions and countries, to final data publication service, one must handle the massive, heterogeneous, and complex data from genetics, imaging, demographics, or clinical scores. These data must be both efficiently obtained and downloadable. We present a Python solution, based on the CubicWeb open-source semantic framework, aimed at building population imaging study repositories. In addition, we focus on the tools developed around this framework to overcome the challenges associated with data sharing and collaborative requirements. We describe a set of three highly adaptive web services that transform the CubicWeb framework into a (1) multi-center upload platform, (2) collaborative quality assessment platform, and (3) publication platform endowed with massive-download capabilities. Two major European projects, IMAGEN and EU-AIMS, are currently supported by the described framework. We also present a Python package that enables end users to remotely query neuroimaging, genetics, and clinical data from scripts. PMID:28360851

Neuroimaging, Genetics, and Clinical Data Sharing in Python Using the CubicWeb Framework.

PubMed

Grigis, Antoine; Goyard, David; Cherbonnier, Robin; Gareau, Thomas; Papadopoulos Orfanos, Dimitri; Chauvat, Nicolas; Di Mascio, Adrien; Schumann, Gunter; Spooren, Will; Murphy, Declan; Frouin, Vincent

2017-01-01

In neurosciences or psychiatry, the emergence of large multi-center population imaging studies raises numerous technological challenges. From distributed data collection, across different institutions and countries, to final data publication service, one must handle the massive, heterogeneous, and complex data from genetics, imaging, demographics, or clinical scores. These data must be both efficiently obtained and downloadable. We present a Python solution, based on the CubicWeb open-source semantic framework, aimed at building population imaging study repositories. In addition, we focus on the tools developed around this framework to overcome the challenges associated with data sharing and collaborative requirements. We describe a set of three highly adaptive web services that transform the CubicWeb framework into a (1) multi-center upload platform, (2) collaborative quality assessment platform, and (3) publication platform endowed with massive-download capabilities. Two major European projects, IMAGEN and EU-AIMS, are currently supported by the described framework. We also present a Python package that enables end users to remotely query neuroimaging, genetics, and clinical data from scripts.

Semantic similarity between ontologies at different scales

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Qingpeng; Haglin, David J.

In the past decade, existing and new knowledge and datasets has been encoded in different ontologies for semantic web and biomedical research. The size of ontologies is often very large in terms of number of concepts and relationships, which makes the analysis of ontologies and the represented knowledge graph computational and time consuming. As the ontologies of various semantic web and biomedical applications usually show explicit hierarchical structures, it is interesting to explore the trade-offs between ontological scales and preservation/precision of results when we analyze ontologies. This paper presents the first effort of examining the capability of this idea viamore » studying the relationship between scaling biomedical ontologies at different levels and the semantic similarity values. We evaluate the semantic similarity between three Gene Ontology slims (Plant, Yeast, and Candida, among which the latter two belong to the same kingdom—Fungi) using four popular measures commonly applied to biomedical ontologies (Resnik, Lin, Jiang-Conrath, and SimRel). The results of this study demonstrate that with proper selection of scaling levels and similarity measures, we can significantly reduce the size of ontologies without losing substantial detail. In particular, the performance of Jiang-Conrath and Lin are more reliable and stable than that of the other two in this experiment, as proven by (a) consistently showing that Yeast and Candida are more similar (as compared to Plant) at different scales, and (b) small deviations of the similarity values after excluding a majority of nodes from several lower scales. This study provides a deeper understanding of the application of semantic similarity to biomedical ontologies, and shed light on how to choose appropriate semantic similarity measures for biomedical engineering.« less

GOOSE: semantic search on internet connected sensors

NASA Astrophysics Data System (ADS)

Schutte, Klamer; Bomhof, Freek; Burghouts, Gertjan; van Diggelen, Jurriaan; Hiemstra, Peter; van't Hof, Jaap; Kraaij, Wessel; Pasman, Huib; Smith, Arthur; Versloot, Corne; de Wit, Joost

2013-05-01

More and more sensors are getting Internet connected. Examples are cameras on cell phones, CCTV cameras for traffic control as well as dedicated security and defense sensor systems. Due to the steadily increasing data volume, human exploitation of all this sensor data is impossible for effective mission execution. Smart access to all sensor data acts as enabler for questions such as "Is there a person behind this building" or "Alert me when a vehicle approaches". The GOOSE concept has the ambition to provide the capability to search semantically for any relevant information within "all" (including imaging) sensor streams in the entire Internet of sensors. This is similar to the capability provided by presently available Internet search engines which enable the retrieval of information on "all" web pages on the Internet. In line with current Internet search engines any indexing services shall be utilized cross-domain. The two main challenge for GOOSE is the Semantic Gap and Scalability. The GOOSE architecture consists of five elements: (1) an online extraction of primitives on each sensor stream; (2) an indexing and search mechanism for these primitives; (3) a ontology based semantic matching module; (4) a top-down hypothesis verification mechanism and (5) a controlling man-machine interface. This paper reports on the initial GOOSE demonstrator, which consists of the MES multimedia analysis platform and the CORTEX action recognition module. It also provides an outlook into future GOOSE development.

Supporting in- and off-Hospital Patient Management Using a Web-based Integrated Software Platform.

PubMed

Spyropoulos, Basile; Botsivali, Maria; Tzavaras, Aris; Pierros, Vasileios

2015-01-01

In this paper, a Web-based software platform appropriately designed to support the continuity of health care information and management for both in and out of hospital care is presented. The system has some additional features as it is the formation of continuity of care records and the transmission of referral letters with a semantically annotated web service. The platform's Web-orientation provides significant advantages, allowing for easily accomplished remote access.

Semantic Annotation of Video Fragments as Learning Objects: A Case Study with "YouTube" Videos and the Gene Ontology

ERIC Educational Resources Information Center

Garcia-Barriocanal, Elena; Sicilia, Miguel-Angel; Sanchez-Alonso, Salvador; Lytras, Miltiadis

2011-01-01

Web 2.0 technologies can be considered a loosely defined set of Web application styles that foster a kind of media consumer more engaged, and usually active in creating and maintaining Internet contents. Thus, Web 2.0 applications have resulted in increased user participation and massive user-generated (or user-published) open multimedia content,…

Bridging Social and Semantic Computing - Design and Evaluation of User Interfaces for Hybrid Systems

ERIC Educational Resources Information Center

Bostandjiev, Svetlin Alex I.

2012-01-01

The evolution of the Web brought new interesting problems to computer scientists that we loosely classify in the fields of social and semantic computing. Social computing is related to two major paradigms: computations carried out by a large amount of people in a collective intelligence fashion (i.e. wikis), and performing computations on social…

Enacting the Semantic Web: Ontological Orderings, Negotiated Standards, and Human-Machine Translations

ERIC Educational Resources Information Center

McCarthy, Matthew T.

2017-01-01

Artificial intelligence (AI) that is based upon semantic search has become one of the dominant means for accessing information in recent years. This is particularly the case in mobile contexts, as search-based AI are embedded in each of the major mobile operating systems. The implications are such that information is becoming less a matter of…

Developing Reflective and Thinking Skills by Means of Semantic Mapping Strategies in Kindergarten Teacher Education.

ERIC Educational Resources Information Center

Lim, Swee Eng; Cheng, Pui Wah Chan; Lam, Mei Seung; Ngan, So Fong

2003-01-01

This study examined some of the affective outcomes for teacher educators and student teachers resulting from the use of semantic webbing/mapping as a strategy for facilitating reflective and critical thinking skills in a kindergarten teacher education program in Hong Kong. Interviews of a random sample of participants and an analysis of their…

Integrating Dynamic Data and Sensors with Semantic 3D City Models in the Context of Smart Cities

NASA Astrophysics Data System (ADS)

Chaturvedi, K.; Kolbe, T. H.

2016-10-01

Smart cities provide effective integration of human, physical and digital systems operating in the built environment. The advancements in city and landscape models, sensor web technologies, and simulation methods play a significant role in city analyses and improving quality of life of citizens and governance of cities. Semantic 3D city models can provide substantial benefits and can become a central information backbone for smart city infrastructures. However, current generation semantic 3D city models are static in nature and do not support dynamic properties and sensor observations. In this paper, we propose a new concept called Dynamizer allowing to represent highly dynamic data and providing a method for injecting dynamic variations of city object properties into the static representation. The approach also provides direct capability to model complex patterns based on statistics and general rules and also, real-time sensor observations. The concept is implemented as an Application Domain Extension for the CityGML standard. However, it could also be applied to other GML-based application schemas including the European INSPIRE data themes and national standards for topography and cadasters like the British Ordnance Survey Mastermap or the German cadaster standard ALKIS.